1
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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] [Grants] [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.
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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
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2
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Konrad SF, Vanderlinden W, Frederickx W, Brouns T, Menze BH, De Feyter S, Lipfert J. High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes. NANOSCALE 2021; 13:5435-5447. [PMID: 33683227 DOI: 10.1039/d0nr08564b] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleosomes, the fundamental units of chromatin, regulate readout and expression of eukaryotic genomes. Single-molecule experiments have revealed force-induced nucleosome accessibility, but a high-resolution unwrapping landscape in the absence of external forces is currently lacking. Here, we introduce a high-throughput pipeline for the analysis of nucleosome conformations based on atomic force microscopy and automated, multi-parameter image analysis. Our data set of ∼10 000 nucleosomes reveals multiple unwrapping states corresponding to steps of 5 bp DNA. For canonical H3 nucleosomes, we observe that dissociation from one side impedes unwrapping from the other side, but in contrast to force-induced unwrapping, we find only a weak sequence-dependent asymmetry. Notably, centromeric CENP-A nucleosomes do not unwrap anti-cooperatively, in stark contrast to H3 nucleosomes. Finally, our results reconcile previous conflicting findings about the differences in height between H3 and CENP-A nucleosomes. We expect our approach to enable critical insights into epigenetic regulation of nucleosome structure and stability and to facilitate future high-throughput AFM studies that involve heterogeneous nucleoprotein complexes.
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Affiliation(s)
- Sebastian F Konrad
- Department of Physics and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany.
| | - Willem Vanderlinden
- Department of Physics and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany.
| | - Wout Frederickx
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Tine Brouns
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Björn H Menze
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Steven De Feyter
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Jan Lipfert
- Department of Physics and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany.
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3
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Mahlke MA, Nechemia-Arbely Y. Guarding the Genome: CENP-A-Chromatin in Health and Cancer. Genes (Basel) 2020; 11:genes11070810. [PMID: 32708729 PMCID: PMC7397030 DOI: 10.3390/genes11070810] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023] Open
Abstract
Faithful chromosome segregation is essential for the maintenance of genomic integrity and requires functional centromeres. Centromeres are epigenetically defined by the histone H3 variant, centromere protein A (CENP-A). Here we highlight current knowledge regarding CENP-A-containing chromatin structure, specification of centromere identity, regulation of CENP-A deposition and possible contribution to cancer formation and/or progression. CENP-A overexpression is common among many cancers and predicts poor prognosis. Overexpression of CENP-A increases rates of CENP-A deposition ectopically at sites of high histone turnover, occluding CCCTC-binding factor (CTCF) binding. Ectopic CENP-A deposition leads to mitotic defects, centromere dysfunction and chromosomal instability (CIN), a hallmark of cancer. CENP-A overexpression is often accompanied by overexpression of its chaperone Holliday Junction Recognition Protein (HJURP), leading to epigenetic addiction in which increased levels of HJURP and CENP-A become necessary to support rapidly dividing p53 deficient cancer cells. Alterations in CENP-A posttranslational modifications are also linked to chromosome segregation errors and CIN. Collectively, CENP-A is pivotal to genomic stability through centromere maintenance, perturbation of which can lead to tumorigenesis.
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Affiliation(s)
- Megan A. Mahlke
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA;
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yael Nechemia-Arbely
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA;
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Correspondence: ; Tel.: +1-412-623-3228; Fax: +1-412-623-7828
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4
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Asymmetric Centromeres Differentially Coordinate with Mitotic Machinery to Ensure Biased Sister Chromatid Segregation in Germline Stem Cells. Cell Stem Cell 2019; 25:666-681.e5. [PMID: 31564548 DOI: 10.1016/j.stem.2019.08.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/25/2019] [Accepted: 08/19/2019] [Indexed: 12/29/2022]
Abstract
Many stem cells utilize asymmetric cell division (ACD) to produce a self-renewed stem cell and a differentiating daughter cell. How non-genic information could be inherited differentially to establish distinct cell fates is not well understood. Here, we report a series of spatiotemporally regulated asymmetric components, which ensure biased sister chromatid attachment and segregation during ACD of Drosophila male germline stem cells (GSCs). First, sister centromeres are differentially enriched with proteins involved in centromere specification and kinetochore function. Second, temporally asymmetric microtubule activities and polarized nuclear envelope breakdown allow for the preferential recognition and attachment of microtubules to asymmetric sister kinetochores and sister centromeres. Abolishment of either the asymmetric sister centromeres or the asymmetric microtubule activities results in randomized sister chromatid segregation. Together, these results provide the cellular basis for partitioning epigenetically distinct sister chromatids during stem cell ACDs, which opens new directions to study these mechanisms in other biological contexts.
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5
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Lawrimore J, Bloom K. The regulation of chromosome segregation via centromere loops. Crit Rev Biochem Mol Biol 2019; 54:352-370. [PMID: 31573359 PMCID: PMC6856439 DOI: 10.1080/10409238.2019.1670130] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/02/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Abstract
Biophysical studies of the yeast centromere have shown that the organization of the centromeric chromatin plays a crucial role in maintaining proper tension between sister kinetochores during mitosis. While centromeric chromatin has traditionally been considered a simple spring, recent work reveals the centromere as a multifaceted, tunable shock absorber. Centromeres can differ from other regions of the genome in their heterochromatin state, supercoiling state, and enrichment of structural maintenance of chromosomes (SMC) protein complexes. Each of these differences can be utilized to alter the effective stiffness of centromeric chromatin. In budding yeast, the SMC protein complexes condensin and cohesin stiffen chromatin by forming and cross-linking chromatin loops, respectively, into a fibrous structure resembling a bottlebrush. The high density of the loops compacts chromatin while spatially isolating the tension from spindle pulling forces to a subset of the chromatin. Paradoxically, the molecular crowding of chromatin via cohesin and condensin also causes an outward/poleward force. The structure allows the centromere to act as a shock absorber that buffers the variable forces generated by dynamic spindle microtubules. Based on the distribution of SMCs from bacteria to human and the conserved distance between sister kinetochores in a wide variety of organisms (0.4 to 1 micron), we propose that the bottlebrush mechanism is the foundational principle for centromere function in eukaryotes.
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Affiliation(s)
- Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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6
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Abstract
Information encoded in DNA is interpreted, modified, and propagated as chromatin. The diversity of inputs encountered by eukaryotic genomes demands a matching capacity for transcriptional outcomes provided by the combinatorial and dynamic nature of epigenetic processes. Advances in genome editing, visualization technology, and genome-wide analyses have revealed unprecedented complexity of chromatin pathways, offering explanations to long-standing questions and presenting new challenges. Here, we review recent findings, exemplified by the emerging understanding of crossregulatory interactions within chromatin, and emphasize the pathologic outcomes of epigenetic misregulation in cancer.
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7
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Chen CC, Mellone BG. Chromatin assembly: Journey to the CENter of the chromosome. J Cell Biol 2017; 214:13-24. [PMID: 27377247 PMCID: PMC4932374 DOI: 10.1083/jcb.201605005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/14/2016] [Indexed: 11/22/2022] Open
Abstract
All eukaryotic genomes are packaged into basic units of DNA wrapped around histone proteins called nucleosomes. The ability of histones to specify a variety of epigenetic states at defined chromatin domains is essential for cell survival. The most distinctive type of chromatin is found at centromeres, which are marked by the centromere-specific histone H3 variant CENP-A. Many of the factors that regulate CENP-A chromatin have been identified; however, our understanding of the mechanisms of centromeric nucleosome assembly, maintenance, and reorganization remains limited. This review discusses recent insights into these processes and draws parallels between centromeric and noncentromeric chromatin assembly mechanisms.
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Affiliation(s)
- Chin-Chi Chen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Barbara G Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
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8
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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.
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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.
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9
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Vlijm R, Kim SH, De Zwart PL, Dalal Y, Dekker C. The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes. NANOSCALE 2017; 9:1862-1870. [PMID: 28094382 PMCID: PMC7959483 DOI: 10.1039/c6nr06245h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness of the DNA wrapping around the nucleosome core is intrinsically ambidextrous, and depends on the pre-assembly supercoiling state of the DNA, i.e., it is not uniquely determined by the octameric histone core. Nucleosomes assembled onto negatively supercoiled DNA are found to exhibit a left-handed conformation, whereas assembly onto positively supercoiled DNA results in right-handed nucleosomes. This intrinsic flexibility to adopt both chiralities is observed both for canonical H3 nucleosomes, and for centromere-specific variant CENP-A nucleosomes. These data support recent advances suggesting an intrinsic adaptability of the nucleosome, and provide insights into how nucleosomes might rapidly re-assemble after cellular processes that generate positive supercoiling in vivo.
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Affiliation(s)
- R Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - S H Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - P L De Zwart
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - Y Dalal
- Chromatin Structure and Epigenetic Mechanisms Unit, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - C Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
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10
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Abstract
Centromeric chromatin undergoes major changes in composition and architecture during each cell cycle. These changes in specialized chromatin facilitate kinetochore formation in mitosis to ensure proper chromosome segregation. Thus, proper orchestration of centromeric chromatin dynamics during interphase, including replication in S phase, is crucial. We provide the current view concerning the centromeric architecture associated with satellite repeat sequences in mammals and its dynamics during the cell cycle. We summarize the contributions of deposited histone variants and their chaperones, other centromeric components - including proteins and their post-translational modifications, and RNAs - and we link the expression and deposition timing of each component during the cell cycle. Because neocentromeres occur at ectopic sites, we highlight how cell cycle processes can go wrong, leading to neocentromere formation and potentially disease.
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Affiliation(s)
- Sebastian Müller
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005 Paris, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005 Paris, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR3664, F-75005 Paris, France
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11
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Musacchio A, Desai A. A Molecular View of Kinetochore Assembly and Function. BIOLOGY 2017; 6:E5. [PMID: 28125021 PMCID: PMC5371998 DOI: 10.3390/biology6010005] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 12/15/2022]
Abstract
Kinetochores are large protein assemblies that connect chromosomes to microtubules of the mitotic and meiotic spindles in order to distribute the replicated genome from a mother cell to its daughters. Kinetochores also control feedback mechanisms responsible for the correction of incorrect microtubule attachments, and for the coordination of chromosome attachment with cell cycle progression. Finally, kinetochores contribute to their own preservation, across generations, at the specific chromosomal loci devoted to host them, the centromeres. They achieve this in most species by exploiting an epigenetic, DNA-sequence-independent mechanism; notable exceptions are budding yeasts where a specific sequence is associated with centromere function. In the last 15 years, extensive progress in the elucidation of the composition of the kinetochore and the identification of various physical and functional modules within its substructure has led to a much deeper molecular understanding of kinetochore organization and the origins of its functional output. Here, we provide a broad summary of this progress, focusing primarily on kinetochores of humans and budding yeast, while highlighting work from other models, and present important unresolved questions for future studies.
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Affiliation(s)
- Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Straße 11, Dortmund 44227, Germany.
- Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen 45117, Germany.
| | - Arshad Desai
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
- Department of Cellular & Molecular Medicine, 9500 Gilman Dr., La Jolla, CA 92093, USA.
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12
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Keçeli BN, De Storme N, Geelen D. In Vivo Ploidy Determination of Arabidopsis thaliana Male and Female Gametophytes. Methods Mol Biol 2017; 1669:77-85. [PMID: 28936651 DOI: 10.1007/978-1-4939-7286-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Organ- or tissue-specific ploidy level determination is often used for answering biological, molecular, genetic, or evolutionary questions in plant sciences. However, current techniques for ploidy determination either cannot provide information on single cell level, require destructive sample preparation, or are laborious and time-consuming. Here, we present a new approach developed in Arabidopsis thaliana, which is not only less labor intensive but also allows in vivo ploidy determination on single cell level. The technique is based on the incorporation of a transgenic construct, consisting of the centromere-specific protein CENH3 fused to the fluorescent reporter GFP that specifically labels centromeric regions and hence allows for an accurate visual determination of the cell's chromosome number. Moreover, by combining the construct with a gametophyte-specific promoter, the technique enables accurate chromosome quantification in all individual gametophytic cell types formed during micro- and mega-gametogenesis. As such, CENH3-based centromere visualization provides an easy and straightforward method to monitor meiotic cell division integrity, gametophytic chromosome dynamics, and reproductive ploidy stability.
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Affiliation(s)
- Burcu Nur Keçeli
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, B-9000, Ghent, Belgium
| | - Nico De Storme
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, B-9000, Ghent, Belgium
| | - Danny Geelen
- In Vitro Biology and Horticulture, Department of Plant Production, Faculty of Bioscience Engineering, University of Ghent, Coupure Links 653, B-9000, Ghent, Belgium.
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13
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CENP-A and H3 Nucleosomes Display a Similar Stability to Force-Mediated Disassembly. PLoS One 2016; 11:e0165078. [PMID: 27820823 PMCID: PMC5098787 DOI: 10.1371/journal.pone.0165078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 10/05/2016] [Indexed: 12/12/2022] Open
Abstract
Centromere-specific nucleosomes are a central feature of the kinetochore complex during mitosis, in which microtubules exert pulling and pushing forces upon the centromere. CENP-A nucleosomes have been assumed to be structurally unique, thereby providing resilience under tension relative to their H3 canonical counterparts. Here, we directly test this hypothesis by subjecting CENP-A and H3 octameric nucleosomes, assembled on random or on centromeric DNA sequences, to varying amounts of applied force by using single-molecule magnetic tweezers. We monitor individual disassembly events of CENP-A and H3 nucleosomes. Regardless of the DNA sequence, the force-mediated disassembly experiments for CENP-A and H3 nucleosomes demonstrate similar rupture forces, life time residency and disassembly steps. From these experiments, we conclude that CENP-A does not, by itself, contribute unique structural features to the nucleosome that lead to a significant resistance against force-mediated disruption. The data present insights into the mechanistic basis for how CENP-A nucleosomes might contribute to the structural foundation of the centromere in vivo.
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14
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Niikura Y, Kitagawa R, Kitagawa K. CENP-A Ubiquitylation Is Inherited through Dimerization between Cell Divisions. Cell Rep 2016; 15:61-76. [PMID: 27052173 DOI: 10.1016/j.celrep.2016.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/26/2016] [Accepted: 02/27/2016] [Indexed: 10/22/2022] Open
Abstract
The presence of chromatin containing the histone H3 variant CENP-A dictates the location of the centromere in a DNA sequence-independent manner. But the mechanism by which centromere inheritance occurs is largely unknown. We previously reported that CENP-A K124 ubiquitylation, mediated by CUL4A-RBX1-COPS8 E3 ligase activity, is required for CENP-A deposition at the centromere. Here, we show that pre-existing ubiquitylated CENP-A is necessary for recruitment of newly synthesized CENP-A to the centromere and that CENP-A ubiquitylation is inherited between cell divisions. In vivo and in vitro analyses using dimerization mutants and dimerization domain fusion mutants revealed that the inheritance of CENP-A ubiquitylation requires CENP-A dimerization. Therefore, we propose models in which CENP-A ubiquitylation is inherited and, through dimerization, determines centromere location. Consistent with this model is our finding that overexpression of a monoubiquitin-fused CENP-A mutant induces neocentromeres at noncentromeric regions of chromosomes.
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Affiliation(s)
- Yohei Niikura
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Risa Kitagawa
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Katsumi Kitagawa
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA; Department of Pediatrics, College of Medicine, The Ohio State University, 700 Children's Drive, Columbus, OH 43205, USA.
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15
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Jeronimo C, Robert F. Histone chaperones FACT and Spt6 prevent histone variants from turning into histone deviants. Bioessays 2016; 38:420-6. [PMID: 26990181 DOI: 10.1002/bies.201500122] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Histone variants are specialized histones which replace their canonical counterparts in specific nucleosomes. Together with histone post-translational modifications and DNA methylation, they contribute to the epigenome. Histone variants are incorporated at specific locations by the concerted action of histone chaperones and ATP-dependent chromatin remodelers. Recent studies have shown that the histone chaperone FACT plays key roles in preventing pervasive incorporation of two histone variants: H2A.Z and CenH3/CENP-A. In addition, Spt6, another histone chaperone, was also shown to be important for appropriate H2A.Z localization. FACT and Spt6 are both associated with elongating RNA polymerase II. Based on these two examples, we propose that the establishment and maintenance of histone variant genomic distributions depend on a transcription-coupled epigenome editing (or surveillance) function of histone chaperones.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
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16
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Giese SH, Fischer L, Rappsilber J. A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides. Mol Cell Proteomics 2016; 15:1094-104. [PMID: 26719564 PMCID: PMC4813691 DOI: 10.1074/mcp.m115.049296] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 12/03/2015] [Indexed: 11/13/2022] Open
Abstract
Cross-linking/mass spectrometry resolves protein-protein interactions or protein folds by help of distance constraints. Cross-linkers with specific properties such as isotope-labeled or collision-induced dissociation (CID)-cleavable cross-linkers are in frequent use to simplify the identification of cross-linked peptides. Here, we analyzed the mass spectrometric behavior of 910 unique cross-linked peptides in high-resolution MS1 and MS2 from published data and validate the observation by a ninefold larger set from currently unpublished data to explore if detailed understanding of their fragmentation behavior would allow computational delivery of information that otherwise would be obtained via isotope labels or CID cleavage of cross-linkers. Isotope-labeled cross-linkers reveal cross-linked and linear fragments in fragmentation spectra. We show that fragment mass and charge alone provide this information, alleviating the need for isotope-labeling for this purpose. Isotope-labeled cross-linkers also indicate cross-linker-containing, albeit not specifically cross-linked, peptides in MS1. We observed that acquisition can be guided to better than twofold enrich cross-linked peptides with minimal losses based on peptide mass and charge alone. By help of CID-cleavable cross-linkers, individual spectra with only linear fragments can be recorded for each peptide in a cross-link. We show that cross-linked fragments of ordinary cross-linked peptides can be linearized computationally and that a simplified subspectrum can be extracted that is enriched in information on one of the two linked peptides. This allows identifying candidates for this peptide in a simplified database search as we propose in a search strategy here. We conclude that the specific behavior of cross-linked peptides in mass spectrometers can be exploited to relax the requirements on cross-linkers.
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Affiliation(s)
- Sven H Giese
- From the ‡Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Lutz Fischer
- §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Juri Rappsilber
- From the ‡Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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17
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Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome. Sci Rep 2015; 5:17038. [PMID: 26602160 PMCID: PMC4658507 DOI: 10.1038/srep17038] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/07/2015] [Indexed: 01/01/2023] Open
Abstract
The centromeric nucleosome is a key epigenetic determinant of centromere identity and function. Consequently, deciphering how CENP-A containing nucleosomes contribute structurally to centromere function is a fundamental question in chromosome biology. Here, we performed microsecond timescale all-atom molecular dynamics (MD) simulations of CENP-A and H3 nucleosomes, and report that the octameric CENP-A core particles and nucleosomes display different dynamics from their canonical H3-containing counterparts. The most significant motion observed is within key interactions at the heart of the CENP-A octameric core, wherein shearing of contacts within the CENP-A:CENP-A' dimerization interface results in a weaker four helix bundle, and an extrusion of 10-30 bp of DNA near the pseudo-dyad. Coupled to other local and global fluctuations, the CENP-A nucleosome occupies a more rugged free energy landscape than the canonical H3 nucleosome. Taken together, our data suggest that CENP-A encodes enhanced distortability to the octameric nucleosome, which may allow for enhanced flexing of the histone core in vivo.
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18
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Díaz-Ingelmo O, Martínez-García B, Segura J, Valdés A, Roca J. DNA Topology and Global Architecture of Point Centromeres. Cell Rep 2015; 13:667-677. [PMID: 26489472 DOI: 10.1016/j.celrep.2015.09.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/08/2015] [Accepted: 09/14/2015] [Indexed: 12/21/2022] Open
Abstract
DNA is wrapped in a left-handed fashion around histone octasomes containing the centromeric histone H3 variant CENP-A. However, DNA topology studies have suggested that DNA is wrapped in a right-handed manner around the CENP-A nucleosome that occupies the yeast point centromere. Here, we determine the DNA linking number difference (ΔLk) stabilized by the yeast centromere and the contribution of the centromere determining elements (CDEI, CDEII, and CDEIII). We show that the intrinsic architecture of the yeast centromere stabilizes +0.6 units of ΔLk. This topology depends on the integrity of CDEII and CDEIII, but it is independent of cbf1 binding to CDEI and of the variable length of CDEII. These findings suggest that the interaction of the CBF3 complex with CDEIII and a distal CDEII segment configures a right-handed DNA loop that excludes CDEI. This loop is then occupied by a CENP-A histone complex, which does not have to be inherently right-handed.
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Affiliation(s)
- Ofelia Díaz-Ingelmo
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Belén Martínez-García
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Antonio Valdés
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain.
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19
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Mattiroli F, D'Arcy S, Luger K. The right place at the right time: chaperoning core histone variants. EMBO Rep 2015; 16:1454-66. [PMID: 26459557 DOI: 10.15252/embr.201540840] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/17/2015] [Indexed: 12/13/2022] Open
Abstract
Histone proteins dynamically regulate chromatin structure and epigenetic signaling to maintain cell homeostasis. These processes require controlled spatial and temporal deposition and eviction of histones by their dedicated chaperones. With the evolution of histone variants, a network of functionally specific histone chaperones has emerged. Molecular details of the determinants of chaperone specificity for different histone variants are only slowly being resolved. A complete understanding of these processes is essential to shed light on the genuine biological roles of histone variants, their chaperones, and their impact on chromatin dynamics.
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Affiliation(s)
- Francesca Mattiroli
- Department of Molecular and Radiobiological Sciences, Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO, USA
| | - Sheena D'Arcy
- Department of Molecular and Radiobiological Sciences, Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO, USA
| | - Karolin Luger
- Department of Molecular and Radiobiological Sciences, Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO, USA
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20
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Melters DP, Nye J, Zhao H, Dalal Y. Chromatin Dynamics in Vivo: A Game of Musical Chairs. Genes (Basel) 2015; 6:751-76. [PMID: 26262644 PMCID: PMC4584328 DOI: 10.3390/genes6030751] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/17/2015] [Accepted: 07/28/2015] [Indexed: 01/30/2023] Open
Abstract
Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. In this review, we will focus on the localization of the major histone variants H3.3, CENP-A, H2A.Z, and macroH2A, as well as how these variants have evolved, their structural differences, and their functional significance in vivo.
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Affiliation(s)
- Daniël P Melters
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Jonathan Nye
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Haiqing Zhao
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA.
| | - Yamini Dalal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
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21
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Westhorpe FG, Fuller CJ, Straight AF. A cell-free CENP-A assembly system defines the chromatin requirements for centromere maintenance. J Cell Biol 2015; 209:789-801. [PMID: 26076692 PMCID: PMC4477859 DOI: 10.1083/jcb.201503132] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/20/2015] [Indexed: 11/22/2022] Open
Abstract
Studying CENP-A nucleosome assembly in a cell-free system defines the role of existing CENP-A nucleosomes in centromere maintenance. Centromeres are defined by the presence of CENP-A nucleosomes in chromatin and are essential for accurate chromosome segregation. Centromeric chromatin epigenetically seeds new CENP-A nucleosome formation, thereby maintaining functional centromeres as cells divide. The features within centromeric chromatin that direct new CENP-A assembly remain unclear. Here, we developed a cell-free CENP-A assembly system that enabled the study of chromatin-bound CENP-A and soluble CENP-A separately. We show that two distinct domains of CENP-A within existing CENP-A nucleosomes are required for new CENP-A assembly and that CENP-A nucleosomes recruit the CENP-A assembly factors CENP-C and M18BP1 independently. Furthermore, we demonstrate that the mechanism of CENP-C recruitment to centromeres is dependent on the density of underlying CENP-A nucleosomes.
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Affiliation(s)
| | - Colin J Fuller
- Department of Biochemistry, Stanford University Medical School, Stanford, CA 94305
| | - Aaron F Straight
- Department of Biochemistry, Stanford University Medical School, Stanford, CA 94305
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22
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Fang J, Liu Y, Wei Y, Deng W, Yu Z, Huang L, Teng Y, Yao T, You Q, Ruan H, Chen P, Xu RM, Li G. Structural transitions of centromeric chromatin regulate the cell cycle-dependent recruitment of CENP-N. Genes Dev 2015; 29:1058-73. [PMID: 25943375 PMCID: PMC4441053 DOI: 10.1101/gad.259432.115] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/13/2015] [Indexed: 11/24/2022]
Abstract
Specific recognition of centromere-specific histone variant CENP-A-containing chromatin by CENP-N is an essential process in the assembly of the kinetochore complex at centromeres prior to mammalian cell division. However, the mechanisms of CENP-N recruitment to centromeres/kinetochores remain unknown. Here, we show that a CENP-A-specific RG loop (Arg80/Gly81) plays an essential and dual regulatory role in this process. The RG loop assists the formation of a compact "ladder-like" structure of CENP-A chromatin, concealing the loop and thus impairing its role in recruiting CENP-N. Upon G1/S-phase transition, however, centromeric chromatin switches from the compact to an open state, enabling the now exposed RG loop to recruit CENP-N prior to cell division. Our results provide the first insights into the mechanisms by which the recruitment of CENP-N is regulated by the structural transitions between compaction and relaxation of centromeric chromatin during the cell cycle.
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Affiliation(s)
- Junnan Fang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuting Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wei
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenqiang Deng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhouliang Yu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Teng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Yao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinglong You
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haihe Ruan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ping Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
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23
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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.
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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
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24
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Abstract
Since discovery of the centromere-specific histone H3 variant CENP-A, centromeres have come to be defined as chromatin structures that establish the assembly site for the complex kinetochore machinery. In most organisms, centromere activity is defined epigenetically, rather than by specific DNA sequences. In this review, we describe selected classic work and recent progress in studies of centromeric chromatin with a focus on vertebrates. We consider possible roles for repetitive DNA sequences found at most centromeres, chromatin factors and modifications that assemble and activate CENP-A chromatin for kinetochore assembly, plus the use of artificial chromosomes and kinetochores to study centromere function.
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Affiliation(s)
- Tatsuo Fukagawa
- Department of Molecular Genetics, National Institute of Genetics and Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan.
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK.
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25
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Biterge B, Schneider R. Histone variants: key players of chromatin. Cell Tissue Res 2014; 356:457-66. [PMID: 24781148 DOI: 10.1007/s00441-014-1862-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/27/2014] [Indexed: 01/01/2023]
Abstract
Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.
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Affiliation(s)
- Burcu Biterge
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404, Illkirch, France
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26
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Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang JP, Henikoff JG. The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. eLife 2014; 3:e01861. [PMID: 24737863 PMCID: PMC3983907 DOI: 10.7554/elife.01861] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In budding yeast, a single cenH3 (Cse4) nucleosome occupies the ∼120-bp functional centromere, however conflicting structural models for the particle have been proposed. To resolve this controversy, we have applied H4S47C-anchored cleavage mapping, which reveals the precise position of histone H4 in every nucleosome in the genome. We find that cleavage patterns at centromeres are unique within the genome and are incompatible with symmetrical structures, including octameric nucleosomes and (Cse4/H4)2 tetrasomes. Centromere cleavage patterns are compatible with a precisely positioned core structure, one in which each of the 16 yeast centromeres is occupied by oppositely oriented Cse4/H4/H2A/H2B hemisomes in two rotational phases within the population. Centromere-specific hemisomes are also inferred from distances observed between closely-spaced H4 cleavages, as predicted from structural modeling. Our results indicate that the orientation and rotational position of the stable hemisome at each yeast centromere is not specified by the functional centromere sequence. DOI:http://dx.doi.org/10.7554/eLife.01861.001 DNA is tightly packaged in cells for a variety of reasons—to allow it to fit inside the nucleus, to protect it from damage, and to help control the production of proteins from genes. The basic unit of packaged DNA is called a nucleosome, which consists of DNA wrapped around a structure formed by two pairs of four different proteins. These proteins, which are called histones, have a role that extends beyond providing structural support for DNA. When cells divide, for example, pairs of ‘sister chromosomes’ are pulled apart to ensure that the two daughter cells both have the same chromosomes as the original cell. The sister chromosomes are pulled apart from a single position called a centromere, and the nucleosomes at this position contain a histone that is different from the histones found everywhere else in the cell. However, until recently it was not clear if the nucleosomes that contained these special cenH3 histones had the same structure as other nucleosomes. Now Henikoff et al. have used a method called H4S47C-anchored cleavage mapping to study every nucleosome in the genome of the yeast S. cerevisiae. This mapping technique uses DNA sequencing to measure the precise distances between fixed points on the DNA in the nucleosome. Knowing these distances tells researchers a great deal about the number and position of the histones within each nucleosome in the genome. Using this approach, Henikoff et al. found that nucleosomes at centromeres are different from other nucleosomes in histone number and arrangement. In particular, the nucleosome at each yeast centromere contains only one each of the four different histones in an asymmetrical orientation, in contrast to all other yeast nucleosomes, which contain two sets of four histones in a symmetrical arrangement. Furthermore, each nucleosome at a centromere can adopt one of two orientations: these orientations are mirror images of each other, and they occur with equal probability. It should also be possible to use the mapping technique developed by Henikoff et al. to study the larger and more complex centromeres found in other organisms, including humans. DOI:http://dx.doi.org/10.7554/eLife.01861.002
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Affiliation(s)
- Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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27
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Dechassa ML, Wyns K, Luger K. Scm3 deposits a (Cse4-H4)2 tetramer onto DNA through a Cse4-H4 dimer intermediate. Nucleic Acids Res 2014; 42:5532-42. [PMID: 24623811 PMCID: PMC4027189 DOI: 10.1093/nar/gku205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The assembly of centromeric nucleosomes is mediated by histone variant-specific chaperones. In budding yeast, the centromere-specific histone H3 variant is Cse4, and the histone chaperone Scm3 functions as a Cse4-specific nucleosome assembly factor. Here, we show that Scm3 exhibits specificity for Cse4-H4, but also interacts with major-type H3-H4 and H2A-H2B. Previously published structures of the Scm3 histone complex demonstrate that Scm3 binds only one copy of Cse4-H4. Consistent with this, we show that Scm3 deposits Cse4-H4 through a dimer intermediate onto deoxyribonucleic acid (DNA) to form a (Cse4-H4)2-DNA complex (tetrasome). Scm3-bound Cse4-H4 does not form a tetramer in the absence of DNA. Moreover, we demonstrate that Cse4 and H3 are structurally compatible to be incorporated in the same nucleosome to form heterotypic particles. Our data shed light on the mechanism of Scm3-mediated nucleosome assembly at the centromere.
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Affiliation(s)
- Mekonnen Lemma Dechassa
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA
| | - Katharina Wyns
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA
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28
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29
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Reply to "CENP-A octamers do not confer a reduction in nucleosome height by AFM". Nat Struct Mol Biol 2014; 21:5-8. [PMID: 24389543 DOI: 10.1038/nsmb.2744] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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30
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Codomo CA, Furuyama T, Henikoff S. CENP-A octamers do not confer a reduction in nucleosome height by AFM. Nat Struct Mol Biol 2014; 21:4-5. [PMID: 24389542 DOI: 10.1038/nsmb.2743] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Christine A Codomo
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Takehito Furuyama
- 1] Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Steven Henikoff
- 1] Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, Seattle, Washington, USA
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31
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A network of players in H3 histone variant deposition and maintenance at centromeres. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:241-50. [DOI: 10.1016/j.bbagrm.2013.11.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 11/14/2013] [Accepted: 11/19/2013] [Indexed: 11/21/2022]
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32
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Geiss CP, Keramisanou D, Sekulic N, Scheffer MP, Black BE, Frangakis AS. CENP-A arrays are more condensed than canonical arrays at low ionic strength. Biophys J 2014; 106:875-82. [PMID: 24559990 PMCID: PMC3944588 DOI: 10.1016/j.bpj.2014.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/02/2014] [Accepted: 01/07/2014] [Indexed: 10/25/2022] Open
Abstract
The centromeric histone H3 variant centromeric protein A (CENP-A), whose sequence is the least conserved among all histone variants, is responsible for specifying the location of the centromere. Here, we present a comprehensive study of CENP-A nucleosome arrays by cryo-electron tomography. We see that CENP-A arrays have different biophysical properties than canonical ones under low ionic conditions, as they are more condensed with a 20% smaller average nearest-neighbor distance and a 30% higher nucleosome density. We find that CENP-A nucleosomes have a predominantly crossed DNA entry/exit site that is narrowed on average by 8°, and they have a propensity to stack face to face. We therefore propose that CENP-A induces geometric constraints at the nucleosome DNA entry/exit site to bring neighboring nucleosomes into close proximity. This specific property of CENP-A may be responsible for generating a fundamental process that contributes to increased chromatin fiber compaction that is propagated under physiological conditions to form centromeric chromatin.
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Affiliation(s)
| | | | - Nikolina Sekulic
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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33
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Lacoste N, Woolfe A, Tachiwana H, Garea AV, Barth T, Cantaloube S, Kurumizaka H, Imhof A, Almouzni G. Mislocalization of the centromeric histone variant CenH3/CENP-A in human cells depends on the chaperone DAXX. Mol Cell 2014; 53:631-44. [PMID: 24530302 DOI: 10.1016/j.molcel.2014.01.018] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 10/02/2013] [Accepted: 01/07/2014] [Indexed: 01/17/2023]
Abstract
Centromeres are essential for ensuring proper chromosome segregation in eukaryotes. Their definition relies on the presence of a centromere-specific H3 histone variant CenH3, known as CENP-A in mammals. Its overexpression in aggressive cancers raises questions concerning its effect on chromatin dynamics and contribution to tumorigenesis. We find that CenH3 overexpression in human cells leads to ectopic enrichment at sites of active histone turnover involving a heterotypic tetramer containing CenH3-H4 with H3.3-H4. Ectopic localization of this particle depends on the H3.3 chaperone DAXX rather than the dedicated CenH3 chaperone HJURP. This aberrant nucleosome occludes CTCF binding and has a minor effect on gene expression. Cells overexpressing CenH3 are more tolerant of DNA damage. Both the survival advantage and CTCF occlusion in these cells are dependent on DAXX. Our findings illustrate how changes in histone variant levels can disrupt chromatin dynamics and suggests a possible mechanism for cell resistance to anticancer treatments.
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Affiliation(s)
- Nicolas Lacoste
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Adam Woolfe
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Hiroaki Tachiwana
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Ana Villar Garea
- Histone Modifications Group, Scientific Coordinator ZfP (Zentrallabor für Proteinanalytik), Adolf Butenandt Institut, University of Munich, Schillerstraße 44, 80336 Munich, Germany
| | - Teresa Barth
- Histone Modifications Group, Scientific Coordinator ZfP (Zentrallabor für Proteinanalytik), Adolf Butenandt Institut, University of Munich, Schillerstraße 44, 80336 Munich, Germany
| | - Sylvain Cantaloube
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Axel Imhof
- Histone Modifications Group, Scientific Coordinator ZfP (Zentrallabor für Proteinanalytik), Adolf Butenandt Institut, University of Munich, Schillerstraße 44, 80336 Munich, Germany
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France.
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Chen CC, Dechassa ML, Bettini E, Ledoux MB, Belisario C, Heun P, Luger K, Mellone BG. CAL1 is the Drosophila CENP-A assembly factor. ACTA ACUST UNITED AC 2014; 204:313-29. [PMID: 24469636 PMCID: PMC3912524 DOI: 10.1083/jcb.201305036] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Representing a unique family of histone assembly factors, CAL1 assembles the histone H3 variant CENP-A on centromeric DNA in Drosophila. Centromeres are specified epigenetically by the incorporation of the histone H3 variant CENP-A. In humans, amphibians, and fungi, CENP-A is deposited at centromeres by the HJURP/Scm3 family of assembly factors, but homologues of these chaperones are absent from a number of major eukaryotic lineages such as insects, fish, nematodes, and plants. In Drosophila, centromeric deposition of CENP-A requires the fly-specific protein CAL1. Here, we show that targeting CAL1 to noncentromeric DNA in Drosophila cells is sufficient to heritably recruit CENP-A, kinetochore proteins, and microtubule attachments. CAL1 selectively interacts with CENP-A and is sufficient to assemble CENP-A nucleosomes that display properties consistent with left-handed octamers. The CENP-A assembly activity of CAL1 resides within an N-terminal domain, whereas the C terminus mediates centromere recognition through an interaction with CENP-C. Collectively, this work identifies the “missing” CENP-A chaperone in flies, revealing fundamental conservation between insect and vertebrate centromere-specification mechanisms.
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Affiliation(s)
- Chin-Chi Chen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
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Walkiewicz MP, Dimitriadis EK, Dalal Y. CENP-A octamers do not confer a reduction in nucleosome height by AFM. Nat Struct Mol Biol 2014; 21:2-3. [PMID: 24389541 PMCID: PMC6756849 DOI: 10.1038/nsmb.2742] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Marcin P Walkiewicz
- National Cancer Institute, National Institutes of Health,
Bethesda Maryland, USA
| | - Emilios K Dimitriadis
- National Institute for BioImaging and BioEngineering,
National Institutes of Health, Bethesda, Maryland, USA
| | - Yamini Dalal
- National Cancer Institute, National Institutes of Health,
Bethesda Maryland, USA
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Catania S, Allshire RC. Anarchic centromeres: deciphering order from apparent chaos. Curr Opin Cell Biol 2013; 26:41-50. [PMID: 24529245 PMCID: PMC3978670 DOI: 10.1016/j.ceb.2013.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/20/2013] [Accepted: 09/24/2013] [Indexed: 12/16/2022]
Abstract
Specialised chromatin in which canonical histone H3 is replaced by CENP-A, an H3 related protein, is a signature of active centromeres and provides the foundation for kinetochore assembly. The location of centromeres is not fixed since centromeres can be inactivated and new centromeres can arise at novel locations independently of specific DNA sequence elements. Therefore, the establishment and maintenance of CENP-A chromatin and kinetochores provide an exquisite example of genuine epigenetic regulation. The composition of CENP-A nucleosomes is contentious but several studies suggest that, like regular H3 particles, they are octamers. Recent analyses have provided insight into how CENP-A is recognised and propagated, identified roles for post-translational modifications and dissected how CENP-A recruits other centromere proteins to mediate kinetochore assembly.
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Affiliation(s)
- Sandra Catania
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, Scotland, UK
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, Scotland, UK.
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Hasson D, Panchenko T, Salimian KJ, Salman MU, Sekulic N, Alonso A, Warburton PE, Black BE. The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol 2013; 20:687-95. [PMID: 23644596 PMCID: PMC3760417 DOI: 10.1038/nsmb.2562] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/07/2013] [Indexed: 12/27/2022]
Abstract
The centromere is the chromosomal locus that ensures fidelity in genome transmission at cell division. Centromere protein A (CENP-A) is a histone H3 variant that specifies centromere location independently of DNA sequence. Conflicting evidence has emerged regarding the histone composition and stoichiometry of CENP-A nucleosomes. Here we show that the predominant form of the CENP-A particle at human centromeres is an octameric nucleosome. CENP-A nucleosomes are very highly phased on α-satellite 171 bp monomers at normal centromeres, and also display strong positioning at neocentromeres. At either type of functional centromere, CENP-A nucleosomes exhibit similar DNA wrapping behavior as octameric CENP-A nucleosomes reconstituted with recombinant components, having looser DNA termini than those on their conventional counterparts containing canonical H3. Thus, the fundamental unit of the chromatin that epigenetically specifies centromere location in mammals is an octameric nucleosome with loose termini.
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Affiliation(s)
- Dan Hasson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Lidsky PV, Sprenger F, Lehner CF. Distinct modes of centromere protein dynamics during cell cycle progression in Drosophila S2R+ cells. J Cell Sci 2013; 126:4782-93. [DOI: 10.1242/jcs.134122] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Centromeres are specified epigenetically in animal cells. Therefore, faithful chromosome inheritance depends critically on the accurate maintenance of epigenetic centromere marks during progression through the cell cycle. Clarification of the mechanisms that control centromere protein behavior during the cell cycle should profit from the relative simplicity of the protein cast at Drosophila centromeres. Thus we have analyzed the dynamics of the three key players Cid/Cenp-A, Cenp-C and Cal1 in S2R+ cells using quantitative microscopy and fluorescence recovery after photobleaching in combination with novel fluorescent cell cycle markers. As revealed by the observed protein abundances and mobilities, centromeres proceed through at least five distinct states during the cell cycle, distinguished in part by unexpected Cid behavior. In addition to the predominant Cid loading onto centromeres during G1, a considerable but transient increase was detected during early mitosis. Low level of Cid loading was detected in late S and G2, starting at the reported time of centromere DNA replication. Our results disclose the complexities of Drosophila centromere protein dynamics and its intricate coordination with cell cycle progression.
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