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Kixmoeller K, Chang YW, Black BE. Centromeric chromatin clearings demarcate the site of kinetochore formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591177. [PMID: 38712116 PMCID: PMC11071481 DOI: 10.1101/2024.04.26.591177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The centromere is the chromosomal locus that recruits the kinetochore, directing faithful propagation of the genome during cell division. The kinetochore has been interrogated by electron microscopy since the middle of the last century, but with methodologies that compromised fine structure. Using cryo-ET on human mitotic chromosomes, we reveal a distinctive architecture at the centromere: clustered 20-25 nm nucleosome-associated complexes within chromatin clearings that delineate them from surrounding chromatin. Centromere components CENP-C and CENP-N are each required for the integrity of the complexes, while CENP-C is also required to maintain the chromatin clearing. We further visualize the scaffold of the fibrous corona, a structure amplified at unattached kinetochores, revealing crescent-shaped parallel arrays of fibrils that extend >1 μm. Thus, we reveal how the organization of centromeric chromatin creates a clearing at the site of kinetochore formation as well as the nature of kinetochore amplification mediated by corona fibrils.
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Affiliation(s)
- Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Biochemistry Biophysics Chemical Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Biochemistry Biophysics Chemical Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, PA, USA
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Biochemistry Biophysics Chemical Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Institute of Structural Biology, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, PA, USA
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2
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Packiaraj J, Thakur J. DNA satellite and chromatin organization at mouse centromeres and pericentromeres. Genome Biol 2024; 25:52. [PMID: 38378611 PMCID: PMC10880262 DOI: 10.1186/s13059-024-03184-z] [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: 06/02/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Centromeres are essential for faithful chromosome segregation during mitosis and meiosis. However, the organization of satellite DNA and chromatin at mouse centromeres and pericentromeres is poorly understood due to the challenges of assembling repetitive genomic regions. RESULTS Using recently available PacBio long-read sequencing data from the C57BL/6 strain, we find that contrary to the previous reports of their homogeneous nature, both centromeric minor satellites and pericentromeric major satellites exhibit a high degree of variation in sequence and organization within and between arrays. While most arrays are continuous, a significant fraction is interspersed with non-satellite sequences, including transposable elements. Using chromatin immunoprecipitation sequencing (ChIP-seq), we find that the occupancy of CENP-A and H3K9me3 chromatin at centromeric and pericentric regions, respectively, is associated with increased sequence enrichment and homogeneity at these regions. The transposable elements at centromeric regions are not part of functional centromeres as they lack significant CENP-A enrichment. Furthermore, both CENP-A and H3K9me3 nucleosomes occupy minor and major satellites spanning centromeric-pericentric junctions and a low yet significant amount of CENP-A spreads locally at centromere junctions on both pericentric and telocentric sides. Finally, while H3K9me3 nucleosomes display a well-phased organization on major satellite arrays, CENP-A nucleosomes on minor satellite arrays are poorly phased. Interestingly, the homogeneous class of major satellites also phase CENP-A and H3K27me3 nucleosomes, indicating that the nucleosome phasing is an inherent property of homogeneous major satellites. CONCLUSIONS Our findings reveal that mouse centromeres and pericentromeres display a high diversity in satellite sequence, organization, and chromatin structure.
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Affiliation(s)
- Jenika Packiaraj
- Department of Biology, Emory University, 1510 Clifton Rd, Atlanta, GA, 30322, USA
| | - Jitendra Thakur
- Department of Biology, Emory University, 1510 Clifton Rd, Atlanta, GA, 30322, USA.
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3
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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] [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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4
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Kale S, Boopathi R, Belotti E, Lone IN, Graies M, Schröder M, Petrova M, Papin C, Bednar J, Ugrinova I, Hamiche A, Dimitrov S. The CENP-A nucleosome: where and when it happens during the inner kinetochore's assembly. Trends Biochem Sci 2023; 48:849-859. [PMID: 37596196 DOI: 10.1016/j.tibs.2023.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023]
Abstract
CENP-A is an essential histone variant that replaces the canonical H3 at the centromeres and marks these regions epigenetically. The CENP-A nucleosome is the specific building block of centromeric chromatin, and it is recognized by CENP-C and CENP-N, two components of the constitutive centromere-associated network (CCAN), the first protein layer of the kinetochore. Recent proposals of the yeast and human (h)CCAN structures position the assembly on exposed DNA, suggesting an elusive spatiotemporal recognition. We summarize the data on the structural organization of the CENP-A nucleosome and the binding of CENP-C and CENP-N. The latter posits an apparent contradiction in engaging the CENP-A nucleosome versus the CCAN. We propose a reconciliatory model for the assembly of CCAN on centromeric chromatin.
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Affiliation(s)
- Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey.
| | - Ramachandran Boopathi
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; Laboratoire de Biologie et de Modelisation de la Cellule (LBMC), CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Edwige Belotti
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - Mohamed Graies
- Institute for Advanced Biosciences, INSERM U1209, CNRS, UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Maria Schröder
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Petrova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Christophe Papin
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Illkirch-Graffenstaden, France
| | - Jan Bednar
- Institute for Advanced Biosciences, INSERM U1209, CNRS, UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Iva Ugrinova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Ali Hamiche
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Illkirch-Graffenstaden, France.
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey; Institute for Advanced Biosciences, INSERM U1209, CNRS, UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
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5
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Packiaraj J, Thakur J. DNA satellite and chromatin organization at house mouse centromeres and pericentromeres. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549612. [PMID: 37503200 PMCID: PMC10370071 DOI: 10.1101/2023.07.18.549612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Centromeres are essential for faithful chromosome segregation during mitosis and meiosis. However, the organization of satellite DNA and chromatin at mouse centromeres and pericentromeres is poorly understood due to the challenges of sequencing and assembling repetitive genomic regions. Using recently available PacBio long-read sequencing data from the C57BL/6 strain and chromatin profiling, we found that contrary to the previous reports of their highly homogeneous nature, centromeric and pericentromeric satellites display varied sequences and organization. We find that both centromeric minor satellites and pericentromeric major satellites exhibited sequence variations within and between arrays. While most arrays are continuous, a significant fraction is interspersed with non-satellite sequences, including transposable elements. Additionally, we investigated CENP-A and H3K9me3 chromatin organization at centromeres and pericentromeres using Chromatin immunoprecipitation sequencing (ChIP-seq). We found that the occupancy of CENP-A and H3K9me3 chromatin at centromeric and pericentric regions, respectively, is associated with increased sequence abundance and homogeneity at these regions. Furthermore, the transposable elements at centromeric regions are not part of functional centromeres as they lack CENP-A enrichment. Finally, we found that while H3K9me3 nucleosomes display a well-phased organization on major satellite arrays, CENP-A nucleosomes on minor satellite arrays lack phased organization. Interestingly, the homogeneous class of major satellites phase CENP-A and H3K27me3 nucleosomes as well, indicating that the nucleosome phasing is an inherent property of homogeneous major satellites. Overall, our findings reveal that house mouse centromeres and pericentromeres, which were previously thought to be highly homogenous, display significant diversity in satellite sequence, organization, and chromatin structure.
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Affiliation(s)
- Jenika Packiaraj
- Department of Biology, Emory University, 1510 Clifton Rd, Atlanta, GA 30322
| | - Jitendra Thakur
- Department of Biology, Emory University, 1510 Clifton Rd, Atlanta, GA 30322
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Li L, Yuan Q, Chu YM, Jiang HY, Zhao JH, Su Q, Huo DQ, Zhang XF. Advances in holliday junction recognition protein (HJURP): Structure, molecular functions, and roles in cancer. Front Cell Dev Biol 2023; 11:1106638. [PMID: 37025176 PMCID: PMC10070699 DOI: 10.3389/fcell.2023.1106638] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
Oncogenes are increasingly recognized as important factors in the development and progression of cancer. Holliday Junction Recognition Protein (HJURP) is a highly specialized mitogenic protein that is a chaperone protein of histone H3. The HJURP gene is located on chromosome 2q37.1 and is involved in nucleosome composition in the mitotic region, forming a three-dimensional crystal structure with Centromere Protein A (CENP-A) and the histone 4 complex. HJURP is involved in the recruitment and assembly of centromere and kinetochore and plays a key role in stabilizing the chromosome structure of tumor cells, and its dysfunction may contribute to tumorigenesis. In the available studies HJURP is upregulated in a variety of cancer tissues and cancer cell lines and is involved in tumor proliferation, invasion, metastasis and immune response. In an in vivo model, overexpression of HJURP in most cancer cell lines promotes cell proliferation and invasiveness, reduces susceptibility to apoptosis, and promotes tumor growth. In addition, upregulation of HJURP was associated with poorer prognosis in a variety of cancers. These properties suggest that HJURP may be a possible target for the treatment of certain cancers. Various studies targeting HJURP as a prognostic and therapeutic target for cancer are gradually attracting interest and attention. This paper reviews the functional and molecular mechanisms of HJURP in a variety of tumor types with the aim of providing new targets for future cancer therapy.
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Affiliation(s)
- Lin Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, China
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
| | - Qiang Yuan
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Yue-Ming Chu
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Hang-Yu Jiang
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Ju-Hua Zhao
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
| | - Qiang Su
- Institute of Tissue Engineering and Stem Cells, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- Nanchong Key Laboratory of Individualized Drug Therapy, Nanchong, China
| | - Dan-Qun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, China
- *Correspondence: Dan-Qun Huo, ; Xiao-Fen Zhang,
| | - Xiao-Fen Zhang
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- *Correspondence: Dan-Qun Huo, ; Xiao-Fen Zhang,
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7
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Morrison O, Thakur J. Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin. Int J Mol Sci 2021; 22:6922. [PMID: 34203193 PMCID: PMC8268097 DOI: 10.3390/ijms22136922] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 01/19/2023] Open
Abstract
Chromatin consists of a complex of DNA and histone proteins as its core components and plays an important role in both packaging DNA and regulating DNA metabolic pathways such as DNA replication, transcription, recombination, and chromosome segregation. Proper functioning of chromatin further involves a network of interactions among molecular complexes that modify chromatin structure and organization to affect the accessibility of DNA to transcription factors leading to the activation or repression of the transcription of target DNA loci. Based on its structure and compaction state, chromatin is categorized into euchromatin, heterochromatin, and centromeric chromatin. In this review, we discuss distinct chromatin factors and molecular complexes that constitute euchromatin-open chromatin structure associated with active transcription; heterochromatin-less accessible chromatin associated with silencing; centromeric chromatin-the site of spindle binding in chromosome segregation.
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Affiliation(s)
| | - Jitendra Thakur
- Department of Biology, Emory University, 1510 Clifton Rd #2006, Atlanta, GA 30322, USA;
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8
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Abstract
In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of DNA is dependent on the chromatin structure and dynamics, which essentially control DNA-related processes, including transcription, DNA replication, and repair. All of the factors that affect the structure and dynamics of nucleosomes, the nucleosome-nucleosome interaction interfaces, and the binding of linker histones or other chromatin-binding proteins need to be considered to understand the organization and function of chromatin fibers. In this review, we provide a summary of recent progress on the structure of chromatin fibers in vitro and in the nucleus, highlight studies on the dynamic regulation of chromatin fibers, and discuss their related biological functions and abnormal organization in diseases.
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Affiliation(s)
- Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China; .,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Wei Li
- National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; .,Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; .,University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation. Nat Commun 2021; 12:1763. [PMID: 33741944 PMCID: PMC7979930 DOI: 10.1038/s41467-021-21985-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 02/22/2021] [Indexed: 11/08/2022] Open
Abstract
Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. The CBF3core specifically recognizes the nucleosomal CCG motif through the Gal4 domain while allosterically altering the DNA conformation. Cryo-EM, modeling, and mutational studies reveal that the CBF3core forms dynamic interactions with core histones H2B and CENP-A in the CEN3 nucleosome. Our results provide insights into the structure of the budding yeast centromeric nucleosome and the mechanism of its assembly, which have implications for analogous processes of human centromeric nucleosome formation.
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10
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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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11
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Melters DP, Dalal Y. Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin. J Mol Biol 2020; 433:166720. [PMID: 33221335 PMCID: PMC8770095 DOI: 10.1016/j.jmb.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/12/2023]
Abstract
Chromatin is the epigenomic platform for diverse nuclear processes such as DNA repair, replication, transcription, telomere, and centromere function. In cancer cells, mutations in key processes result in DNA amplification, chromosome translocations, and chromothripsis, severely distorting the natural chromatin state. In normal and diseased states, dozens of chromatin effectors alter the physical integrity and dynamics of chromatin at the level of both single nucleosomes and arrays of nucleosomes folded into 3-dimensional shapes. Integrating these length scales, from the 10 nm sized nucleosome to mitotic chromosomes, whilst jostling within the crowded environment of the cell, cannot yet be achieved by a single technology. In this review, we discuss tools that have proven powerful in the investigation of nucleosome and chromatin fiber dynamics. We also provide a deeper focus into atomic force microscopy (AFM) applications that can bridge diverse length and time scales. Using time course AFM, we observe that chromatin condensation by H1.5 is dynamic, whereas using nano-indentation force spectroscopy we observe that both histone variants and nucleosome binding partners alter material properties of individual nucleosomes. Finally, we demonstrate how high-speed AFM can visualize plasmid DNA dynamics, intermittent nucleosome-nucleosome contacts, and changes in nucleosome phasing along a contiguous chromatin fiber. Altogether, the development of innovative technologies holds the promise of revealing the secret lives of nucleosomes, potentially bridging the gaps in our understanding of how chromatin works within living cells and tissues.
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Affiliation(s)
- Daniël P Melters
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
| | - Yamini Dalal
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
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12
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Feng Y, Endo M, Sugiyama H. Nucleosomes and Epigenetics from a Chemical Perspective. Chembiochem 2020; 22:595-612. [PMID: 32864867 DOI: 10.1002/cbic.202000332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/26/2020] [Indexed: 12/19/2022]
Abstract
Nucleosomes, which are the fundamental building blocks of chromatin, are highly dynamic, they play vital roles in the formation of higher-order chromatin structures and orchestrate gene regulation. Nucleosome structures, histone modifications, nucleosome-binding proteins, and their functions are being gradually unravelled with the development of epigenetics. With the continuous development of research approaches such as cryo-EM, FRET and next-generation sequencing for genome-wide analysis of nucleosomes, the understanding of nucleosomes is getting wider and deeper. Herein, we review recent progress in research on nucleosomes and epigenetics, from nucleosome structure to chromatin formation, with a focus on chemical aspects. Basic knowledge of the nucleosome (nucleosome structure, nucleosome position sequence, nucleosome assembly and remodeling), epigenetic modifications, chromatin structure, chemical biology methods and nucleosome, observation nucleosome by AFM, phase separation and nucleosomes are described in this review.
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Affiliation(s)
- Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
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13
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Mitra S, Srinivasan B, Jansen LE. Stable inheritance of CENP-A chromatin: Inner strength versus dynamic control. J Cell Biol 2020; 219:e202005099. [PMID: 32931551 PMCID: PMC7659725 DOI: 10.1083/jcb.202005099] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022] Open
Abstract
Chromosome segregation during cell division is driven by mitotic spindle attachment to the centromere region on each chromosome. Centromeres form a protein scaffold defined by chromatin featuring CENP-A, a conserved histone H3 variant, in a manner largely independent of local DNA cis elements. CENP-A nucleosomes fulfill two essential criteria to epigenetically identify the centromere. They undergo self-templated duplication to reestablish centromeric chromatin following DNA replication. More importantly, CENP-A incorporated into centromeric chromatin is stably transmitted through consecutive cell division cycles. CENP-A nucleosomes have unique structural properties and binding partners that potentially explain their long lifetime in vivo. However, rather than a static building block, centromeric chromatin is dynamically regulated throughout the cell cycle, indicating that CENP-A stability is also controlled by external factors. We discuss recent insights and identify the outstanding questions on how dynamic control of the long-term stability of CENP-A ensures epigenetic centromere inheritance.
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Affiliation(s)
- Sreyoshi Mitra
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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14
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Boopathi R, Danev R, Khoshouei M, Kale S, Nahata S, Ramos L, Angelov D, Dimitrov S, Hamiche A, Petosa C, Bednar J. Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends. Nucleic Acids Res 2020; 48:5735-5748. [PMID: 32313946 PMCID: PMC7261176 DOI: 10.1093/nar/gkaa246] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/11/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
The histone H3 variant CENP-A marks centromeres epigenetically and is essential for mitotic fidelity. Previous crystallographic studies of the CENP-A nucleosome core particle (NCP) reconstituted with a human α-satellite DNA derivative revealed both DNA ends to be highly flexible, a feature important for CENP-A mitotic functions. However, recent cryo-EM studies of CENP-A NCP complexes comprising primarily Widom 601 DNA reported well-ordered DNA ends. Here, we report the cryo-EM structure of the CENP-A 601 NCP determined by Volta phase-plate imaging. The data reveal that one (‘left’) 601 DNA end is well ordered whereas the other (‘right’) end is flexible and partly detached from the histone core, suggesting sequence-dependent dynamics of the DNA termini. Indeed, a molecular dynamics simulation of the CENP-A 601 NCP confirmed the distinct dynamics of the two DNA extremities. Reprocessing the image data using two-fold symmetry yielded a cryo-EM map in which both DNA ends appeared well ordered, indicating that such an artefact may inadvertently arise if NCP asymmetry is lost during image processing. These findings enhance our understanding of the dynamic features that discriminate CENP-A from H3 nucleosomes by revealing that DNA end flexibility can be fine-tuned in a sequence-dependent manner.
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Affiliation(s)
- Ramachandran Boopathi
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Radostin Danev
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Maryam Khoshouei
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Seyit Kale
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - Sunil Nahata
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Lorrie Ramos
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Dimitar Angelov
- Laboratoire de Biologie et de Modélisation de la Cellule (LBMC), CNRS/ ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
- Correspondence may also be addressed to Stefan Dimitrov.
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/ CNRS/INSERM, 67404 Illkirch Cedex, France
- Correspondence may also be addressed to Ali Hamiche.
| | - Carlo Petosa
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
- Correspondence may also be addressed to Carlo Petosa.
| | - Jan Bednar
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
- Laboratory of the Biology and Pathology of the Eye, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General Teaching Hospital, 128 00 Prague, Czech Republic
- To whom correspondence should be addressed. Tel: +33 4 76 54 94 73;
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15
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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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16
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Kixmoeller K, Allu PK, Black BE. The centromere comes into focus: from CENP-A nucleosomes to kinetochore connections with the spindle. Open Biol 2020; 10:200051. [PMID: 32516549 PMCID: PMC7333888 DOI: 10.1098/rsob.200051] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic chromosome segregation relies upon specific connections from DNA to the microtubule-based spindle that forms at cell division. The chromosomal locus that directs this process is the centromere, where a structure called the kinetochore forms upon entry into mitosis. Recent crystallography and single-particle electron microscopy have provided unprecedented high-resolution views of the molecular complexes involved in this process. The centromere is epigenetically specified by nucleosomes harbouring a histone H3 variant, CENP-A, and we review recent progress on how it differentiates centromeric chromatin from the rest of the chromosome, the biochemical pathway that mediates its assembly and how two non-histone components of the centromere specifically recognize CENP-A nucleosomes. The core centromeric nucleosome complex (CCNC) is required to recruit a 16-subunit complex termed the constitutive centromere associated network (CCAN), and we highlight recent structures reported of the budding yeast CCAN. Finally, the structures of multiple modular sub-complexes of the kinetochore have been solved at near-atomic resolution, providing insight into how connections are made to the CCAN on one end and to the spindle microtubules on the other. One can now build molecular models from the DNA through to the physical connections to microtubules.
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Affiliation(s)
- Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Praveen Kumar Allu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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17
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Serag MF, Aikeremu A, Tsukamoto R, Piwoński H, Abadi M, Kaji N, Dwyer JR, Baba Y, Habuchi S. Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution. ACS NANO 2019; 13:8155-8168. [PMID: 31244030 DOI: 10.1021/acsnano.9b03259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Histones are basic protein monomers capable of interacting with DNA, providing the mechanism of DNA compaction inside the cell nucleus. The well-ordered assembly process of histone and DNA is a potential candidate as the approach for building DNA-protein nanostructures. Here, utilizing the sequence-independent histone-DNA interaction, we present an approach to self-assemble histones and single-stranded DNA (ssDNA) to form well-defined histone-DNA (sHD) nanoparticles and their multidimensional cross-linked complexes (cHD). By using various molecular biology and microscopy techniques, we elucidate the structure of these complexes, and we show that they are formed at carefully controlled conditions of temperature, ionic strength, concentration, and incubation time. We also demonstrate using a set of ssDNA molecular rulers and a geometric accommodation model that the assembly of sHD and cHD particles proceeds with precise geometry so that the number of ssDNA in these particles can be programmed by the length of ssDNA. We further show that the formation of cHD amplifies the effect of the length of ssDNA on the self-assembly, allowing for distinguishing ssDNA of different lengths at single nucleotide resolution. We envision that our geometry-directed approach of self-assembling histone-DNA nanostructures and the fundamental insights can serve as a structural platform to advance building precisely ordered DNA-protein nanostructures.
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Affiliation(s)
- Maged F Serag
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - Aimaiti Aikeremu
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Ryoko Tsukamoto
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - Hubert Piwoński
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Maram Abadi
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Noritada Kaji
- Department of Applied Chemistry, Graduate School of Engineering , Kyushu University , 744 Motooka , Nishi-ku, Fukuoka 819-0395 , Japan
- JST, PRESTO , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Jason R Dwyer
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- National Institute of Advanced Industrial Science and Technology (AIST) , Takamatsu 761-0395 , Japan
- School of Pharmacy , Kaohsiung Medical University , Kaohsiung 807 , Taiwan , R.O.C
| | - Satoshi Habuchi
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
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18
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Zhao H, Winogradoff D, Dalal Y, Papoian GA. The Oligomerization Landscape of Histones. Biophys J 2019; 116:1845-1855. [PMID: 31005236 DOI: 10.1016/j.bpj.2019.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 12/29/2022] Open
Abstract
In eukaryotes, DNA is packaged within nucleosomes. The DNA of each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Here, we investigate canonical histone assembly and that of the centromere-specific histone variant, centromere protein A (CENP-A), using molecular dynamics simulations. We quantitatively characterize their thermodynamical and dynamical features, showing that two H3/H4 dimers form a structurally floppy, weakly bound complex, the latter exhibiting large instability around the central interface manifested via a swiveling motion of two halves. This finding is consistent with the recently observed DNA handedness flipping of the tetrasome. In contrast, the variant CENP-A encodes distinctive stability to its tetramer with a rigid but twisted interface compared to the crystal structure, implying diverse structural possibilities of the histone variant. Interestingly, the observed tetramer dynamics alter significantly and appear to reach a new balance when H2A/H2B dimers are present. Furthermore, we found that the preferred structure for the (CENP-A/H4)2 tetramer is incongruent with the octameric structure, explaining many of the unusual dynamical behaviors of the CENP-A nucleosome. In all, these data reveal key mechanistic insights and structural details for the assembly of canonical and variant histone tetramers and octamers, providing theoretical quantifications and physical interpretations for longstanding and recent experimental observations. Based on these findings, we propose different chaperone-assisted binding and nucleosome assembly mechanisms for the canonical and CENP-A histone oligomers.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David Winogradoff
- Chemical Physics Program, Institute for Physical Science and Technology
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Garegin A Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Chemical Physics Program, Institute for Physical Science and Technology; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland.
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19
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Novel genetic tools for probing individual H3 molecules in each nucleosome. Curr Genet 2018; 65:371-377. [PMID: 30478690 DOI: 10.1007/s00294-018-0910-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
Abstract
In eukaryotes, genomic DNA is packaged into the nucleus together with histone proteins, forming chromatin. The fundamental repeating unit of chromatin is the nucleosome, a naturally symmetric structure that wraps DNA and is the substrate for numerous regulatory post-translational modifications. However, the biological significance of nucleosomal symmetry until recently had been unexplored. To investigate this issue, we developed an obligate pair of histone H3 heterodimers, a novel genetic tool that allowed us to modulate modification sites on individual H3 molecules within nucleosomes in vivo. We used these constructs for molecular genetic studies, for example demonstrating that H3K36 methylation on a single H3 molecule per nucleosome in vivo is sufficient to restrain cryptic transcription. We also used asymmetric nucleosomes for mass spectrometric analysis of dependency relationships among histone modifications. Furthermore, we extended this system to the centromeric H3 isoform (Cse4/CENP-A), gaining insights into centromeric nucleosomal symmetry and structure. In this review, we summarize our findings and discuss the utility of this novel approach.
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20
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Ichikawa Y, Saitoh N, Kaufman PD. An asymmetric centromeric nucleosome. eLife 2018; 7:37911. [PMID: 30136924 PMCID: PMC6125124 DOI: 10.7554/elife.37911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/22/2018] [Indexed: 02/03/2023] Open
Abstract
Nucleosomes contain two copies of each core histone, held together by a naturally symmetric, homodimeric histone H3-H3 interface. This symmetry has complicated efforts to determine the regulatory potential of this architecture. Through molecular design and in vivo selection, we recently generated obligately heterodimeric H3s, providing a powerful tool for discovery of the degree to which nucleosome symmetry regulates chromosomal functions in living cells (Ichikawa et al., 2017). We now have extended this tool to the centromeric H3 isoform (Cse4/CENP-A) in budding yeast. These studies indicate that a single Cse4 N- or C-terminal extension per pair of Cse4 molecules is sufficient for kinetochore function, and validate previous experiments indicating that an octameric centromeric nucleosome is required for viability in this organism. These data also support the generality of the H3 asymmetric interface for probing general questions in chromatin biology.
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Affiliation(s)
- Yuichi Ichikawa
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States.,Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Paul D Kaufman
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
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21
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Zhang W, Lukoyanova N, Miah S, Lucas J, Vaughan CK. Insights into Centromere DNA Bending Revealed by the Cryo-EM Structure of the Core Centromere Binding Factor 3 with Ndc10. Cell Rep 2018; 24:744-754. [PMID: 30021170 PMCID: PMC6077249 DOI: 10.1016/j.celrep.2018.06.068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/06/2018] [Accepted: 06/15/2018] [Indexed: 12/21/2022] Open
Abstract
The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the kinetochore in these organisms, as it facilitates genetic centromere specification and allows association of all other kinetochore components. We determined high-resolution structures of the core complex of CBF3 alone and in association with a monomeric construct of Ndc10, using cryoelectron microscopy (cryo-EM). We identify the DNA-binding site of the complex and present a model in which CBF3 induces a tight bend in centromeric DNA, thus facilitating assembly of the centromeric nucleosome. Cryo-EM studies of CBF3 reveal the core complex has a deep asymmetric channel The size, conservation, and charge of the channel suggest that it binds centromere DNA Unique insertions in the Ctf13 F box provide the binding site for one Ndc10 monomer The Ndc10 DNA-binding site is in plane with and perpendicular to the CBF3 channel
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Affiliation(s)
- Wenjuan Zhang
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Natalya Lukoyanova
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Shomon Miah
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Jonathan Lucas
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Cara K Vaughan
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
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22
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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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23
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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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24
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How does chromatin package DNA within nucleus and regulate gene expression? Int J Biol Macromol 2017; 101:862-881. [PMID: 28366861 DOI: 10.1016/j.ijbiomac.2017.03.165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
Abstract
The human body is made up of 60 trillion cells, each cell containing 2 millions of genomic DNA in its nucleus. How is this genomic deoxyribonucleic acid [DNA] organised into nuclei? Around 1880, W. Flemming discovered a nuclear substance that was clearly visible on staining under primitive light microscopes and named it 'chromatin'; this is now thought to be the basic unit of genomic DNA organization. Since long before DNA was known to carry genetic information, chromatin has fascinated biologists. DNA has a negatively charged phosphate backbone that produces electrostatic repulsion between adjacent DNA regions, making it difficult for DNA to fold upon itself. In this article, we will try to shed light on how does chromatin package DNA within nucleus and regulate gene expression?
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25
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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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26
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Nechemia-Arbely Y, Fachinetti D, Miga KH, Sekulic N, Soni GV, Kim DH, Wong AK, Lee AY, Nguyen K, Dekker C, Ren B, Black BE, Cleveland DW. Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points. J Cell Biol 2017; 216:607-621. [PMID: 28235947 PMCID: PMC5350519 DOI: 10.1083/jcb.201608083] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/18/2016] [Accepted: 01/17/2017] [Indexed: 12/11/2022] Open
Abstract
In this study, the authors use new reference models for 23 human centromeres and find that at all cell cycle phases centromeric CENP-A chromatin complexes are octameric nucleosomes with two molecules of CENP-A. This finding refutes previous models that have suggested that hemisomes may briefly transition to octameric nucleosomes. Chromatin assembled with centromere protein A (CENP-A) is the epigenetic mark of centromere identity. Using new reference models, we now identify sites of CENP-A and histone H3.1 binding within the megabase, α-satellite repeat–containing centromeres of 23 human chromosomes. The overwhelming majority (97%) of α-satellite DNA is found to be assembled with histone H3.1–containing nucleosomes with wrapped DNA termini. In both G1 and G2 cell cycle phases, the 2–4% of α-satellite assembled with CENP-A protects DNA lengths centered on 133 bp, consistent with octameric nucleosomes with DNA unwrapping at entry and exit. CENP-A chromatin is shown to contain equimolar amounts of CENP-A and histones H2A, H2B, and H4, with no H3. Solid-state nanopore analyses show it to be nucleosomal in size. Thus, in contrast to models for hemisomes that briefly transition to octameric nucleosomes at specific cell cycle points or heterotypic nucleosomes containing both CENP-A and histone H3, human CENP-A chromatin complexes are octameric nucleosomes with two molecules of CENP-A at all cell cycle phases.
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Affiliation(s)
- Yael Nechemia-Arbely
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Daniele Fachinetti
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Karen H Miga
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Nikolina Sekulic
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gautam V Soni
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Dong Hyun Kim
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Adeline K Wong
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Ah Young Lee
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Kristen Nguyen
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Bing Ren
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Don W Cleveland
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093
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27
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Moreno-Moreno O, Torras-Llort M, Azorín F. Variations on a nucleosome theme: The structural basis of centromere function. Bioessays 2017; 39. [PMID: 28220502 DOI: 10.1002/bies.201600241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The centromere is a specialized chromosomal structure that dictates kinetochore assembly and, thus, is essential for accurate chromosome segregation. Centromere identity is determined epigenetically by the presence of a centromere-specific histone H3 variant, CENP-A, that replaces canonical H3 in centromeric chromatin. Here, we discuss recent work by Roulland et al. that identifies structural elements of the nucleosome as essential determinants of centromere function. In particular, CENP-A nucleosomes have flexible DNA ends due to the short αN helix of CENP-A. The higher flexibility of the DNA ends of centromeric nucleosomes impairs binding of linker histones H1, while it facilitates binding of other essential centromeric proteins, such as CENP-C, and is required for mitotic fidelity. This work extends previous observations indicating that the differential structural properties of CENP-A nucleosomes are on the basis of its contribution to centromere identity and function. Here, we discuss the implications of this work and the questions arising from it.
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Affiliation(s)
- Olga Moreno-Moreno
- Institute of Molecular Biology of Barcelona, CSIC, Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Mònica Torras-Llort
- Institute of Molecular Biology of Barcelona, CSIC, Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Barcelona, Spain.,Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute for Science and Technology, Barcelona, Spain
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28
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Adkins NL, Swygert SG, Kaur P, Niu H, Grigoryev SA, Sung P, Wang H, Peterson CL. Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair. J Biol Chem 2017; 292:5271-5281. [PMID: 28202543 DOI: 10.1074/jbc.m117.776369] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/13/2017] [Indexed: 11/06/2022] Open
Abstract
Repair of DNA double strand breaks (DSBs) is key for maintenance of genome integrity. When DSBs are repaired by homologous recombination, DNA ends can undergo extensive processing, producing long stretches of single-stranded DNA (ssDNA). In vivo, DSB processing occurs in the context of chromatin, and studies indicate that histones may remain associated with processed DSBs. Here we demonstrate that histones are not evicted from ssDNA after in vitro chromatin resection. In addition, we reconstitute histone-ssDNA complexes (termed ssNucs) with ssDNA and recombinant histones and analyze these particles by a combination of native gel electrophoresis, sedimentation velocity, electron microscopy, and a recently developed electrostatic force microscopy technique, DREEM (dual-resonance frequency-enhanced electrostatic force microscopy). The reconstituted ssNucs are homogenous and relatively stable, and DREEM reveals ssDNA wrapping around histones. We also find that histone octamers are easily transferred in trans from ssNucs to either double-stranded DNA or ssDNA. Furthermore, the Fun30 remodeling enzyme, which has been implicated in DNA repair, binds ssNucs preferentially over nucleosomes, and ssNucs are effective at activating Fun30 ATPase activity. Our results indicate that ssNucs may be a hallmark of processes that generate ssDNA, and that posttranslational modification of ssNucs may generate novel signaling platforms involved in genome stability.
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Affiliation(s)
- Nicholas L Adkins
- From the Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Sarah G Swygert
- From the Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Parminder Kaur
- the Department of Physics.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
| | - Hengyao Niu
- the Department Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
| | - Sergei A Grigoryev
- the Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Patrick Sung
- the Department Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
| | - Hong Wang
- the Department of Physics.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
| | - Craig L Peterson
- From the Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605,
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29
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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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30
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Bloom K, Costanzo V. Centromere Structure and Function. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:515-539. [PMID: 28840251 DOI: 10.1007/978-3-319-58592-5_21] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The centromere is the genetic locus that specifies the site of kinetochore assembly, where the chromosome will attach to the kinetochore microtubule. The pericentromere is the physical region responsible for the geometry of bi-oriented sister kinetochores in metaphase. In budding yeast the 125 bp point centromere is sufficient to specify kinetochore assembly. The flanking region is enriched (3X) in cohesin and condensin relative to the remaining chromosome arms. The enrichment spans about 30-50 kb around each centromere. We refer to the flanking chromatin as the pericentromere in yeast. In mammals, a 5-10 Mb region dictates where the kinetochore is built. The kinetochore interacts with a very small fraction of DNA on the surface of the centromeric region. The remainder of the centromere lies between the sister kinetochores. This is typically called centromere chromatin. The chromatin sites that directly interface to microtubules cannot be identified due to the repeated sequence within the mammalian centromere. However in both yeast and mammals, the total amount of DNA between the sites of microtubule attachment in metaphase is highly conserved. In yeast the 16 chromosomes are clustered into a 250 nm diameter region, and 800 kb (16 × 50 kb) or ~1 Mb of DNA lies between sister kinetochores. In mammals, 5-10 Mb lies between sister kinetochores. In both organisms the sister kinetochores are separated by about 1 μm. Thus, centromeres of different organisms differ in how they specify kinetochore assembly, but there may be important centromere chromatin functions that are conserved throughout phylogeny. Recently, centromeric chromatin has been reconstituted in vitro using alpha satellite DNA revealing unexpected features of centromeric DNA organization, replication, and response to stress. We will focus on the conserved features of centromere in this review.
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Affiliation(s)
- Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, 623 Fordham Hall CB#3280, Chapel Hill, NC, 27599-3280, USA.
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM, The FIRC Institute of Molecular Oncology, Vai Adamello 16, 21139, Milan, Italy
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31
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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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32
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Ordu O, Lusser A, Dekker NH. Recent insights from in vitro single-molecule studies into nucleosome structure and dynamics. Biophys Rev 2016; 8:33-49. [PMID: 28058066 PMCID: PMC5167136 DOI: 10.1007/s12551-016-0212-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/17/2016] [Indexed: 01/04/2023] Open
Abstract
Eukaryotic DNA is tightly packed into a hierarchically ordered structure called chromatin in order to fit into the micron-scaled nucleus. The basic unit of chromatin is the nucleosome, which consists of a short piece of DNA wrapped around a core of eight histone proteins. In addition to their role in packaging DNA, nucleosomes impact the regulation of essential nuclear processes such as replication, transcription, and repair by controlling the accessibility of DNA. Thus, knowledge of this fundamental DNA-protein complex is crucial for understanding the mechanisms of gene control. While structural and biochemical studies over the past few decades have provided key insights into both the molecular composition and functional aspects of nucleosomes, these approaches necessarily average over large populations and times. In contrast, single-molecule methods are capable of revealing features of subpopulations and dynamic changes in the structure or function of biomolecules, rendering them a powerful complementary tool for probing mechanistic aspects of DNA-protein interactions. In this review, we highlight how these single-molecule approaches have recently yielded new insights into nucleosomal and subnucleosomal structures and dynamics.
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Affiliation(s)
- Orkide Ordu
- Bionanoscience Department, Kavli Institute of Nanoscience,, Delft University of Technology, Van der Maasweg 9,, 2629 HZ Delft, The Netherlands
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Nynke H. Dekker
- Bionanoscience Department, Kavli Institute of Nanoscience,, Delft University of Technology, Van der Maasweg 9,, 2629 HZ Delft, The Netherlands
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33
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Zhao H, Winogradoff D, Bui M, Dalal Y, Papoian GA. Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones. J Am Chem Soc 2016; 138:13207-13218. [PMID: 27454815 PMCID: PMC7757119 DOI: 10.1021/jacs.6b05355] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Histone proteins are essential for the organization, expression, and inheritance of genetic material for eukaryotic cells. A centromere-specific H3 histone variant, centromere protein A (CENP-A), shares about 50% amino acid sequence identity with H3. CENP-A is required for packaging the centromere and for the proper separation of chromosomes during mitosis. Despite their distinct biological functions, previously reported crystal structures of the CENP-A/H4 and H3/H4 dimers reveal a high degree of similarity. In this work, we characterize the structural dynamics of CENP-A/H4 and H3/H4 dimers based on a dual-resolution approach, using both microsecond-scale explicit-solvent all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. Our data show that the H4 histone is significantly more rigid compared with the H3 histone and its variant CENP-A, hence, serving as a reinforcing structural element within the histone core. We report that the CENP-A/H4 dimer is significantly more dynamic than its canonical counterpart H3/H4, and our results provide a physical explanation for this flexibility. Further, we observe that the centromere-specific chaperone Holliday Junction Recognition Protein (HJURP) stabilizes the CENP-A/H4 dimer by forming a specific electrostatic interaction network. Finally, replacing CENP-A S68 with E68 disrupts the binding interface between CENP-A and HJURP in all-atom MD simulation, and consistently, in vivo experiments demonstrate that replacing CENP-A S68 with E68 disrupts CENP-A's localization to the centromere. Based on all our results, we propose that, during the CENP-A/H4 deposition process, the chaperone HJURP protects various substructures of the dimer, serving both as a folding and binding chaperone.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David Winogradoff
- Chemical Physics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Minh Bui
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Garegin A. Papoian
- Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
- Chemical Physics Program, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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34
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Almouzni G, Cedar H. Maintenance of Epigenetic Information. Cold Spring Harb Perspect Biol 2016; 8:8/5/a019372. [PMID: 27141050 DOI: 10.1101/cshperspect.a019372] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The genome is subject to a diverse array of epigenetic modifications from DNA methylation to histone posttranslational changes. Many of these marks are somatically stable through cell division. This article focuses on our knowledge of the mechanisms governing the inheritance of epigenetic marks, particularly, repressive ones, when the DNA and chromatin template are duplicated in S phase. This involves the action of histone chaperones, nucleosome-remodeling enzymes, histone and DNA methylation binding proteins, and chromatin-modifying enzymes. Last, the timing of DNA replication is discussed, including the question of whether this constitutes an epigenetic mark that facilitates the propagation of epigenetic marks.
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Affiliation(s)
- Geneviève Almouzni
- Department of Nuclear Dynamics and Genome Plasticity, Institut Curie, Section de recherche, 75231 Paris Cedex 05, France
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Ein Kerem, Jerusalem, Israel 91120
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35
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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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36
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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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37
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Zhao H, Zhu X, Wang K, Gent JI, Zhang W, Dawe RK, Jiang J. Gene Expression and Chromatin Modifications Associated with Maize Centromeres. G3 (BETHESDA, MD.) 2015; 6:183-92. [PMID: 26564952 PMCID: PMC4704717 DOI: 10.1534/g3.115.022764] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/09/2015] [Indexed: 12/23/2022]
Abstract
Centromeres are defined by the presence of CENH3, a variant of histone H3. Centromeres in most plant species contain exclusively highly repetitive DNA sequences, which has hindered research on structure and function of centromeric chromatin. Several maize centromeres have been nearly completely sequenced, providing a sequence-based platform for genomic and epigenomic research of plant centromeres. Here we report a high resolution map of CENH3 nucleosomes in the maize genome. Although CENH3 nucleosomes are spaced ∼190 bp on average, CENH3 nucleosomes that occupied CentC, a 156-bp centromeric satellite repeat, showed clear positioning aligning with CentC monomers. Maize centromeres contain alternating CENH3-enriched and CENH3-depleted subdomains, which account for 87% and 13% of the centromeres, respectively. A number of annotated genes were identified in the centromeres, including 11 active genes that were located exclusively in CENH3-depleted subdomains. The euchromatic histone modification marks, including H3K4me3, H3K36me3 and H3K9ac, detected in maize centromeres were associated mainly with the active genes. Interestingly, maize centromeres also have lower levels of the heterochromatin histone modification mark H3K27me2 relative to pericentromeric regions. We conclude that neither H3K27me2 nor the three euchromatic histone modifications are likely to serve as functionally important epigenetic marks of centromere identity in maize.
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Affiliation(s)
- Hainan Zhao
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Xiaobiao Zhu
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Kai Wang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706
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38
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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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39
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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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40
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Schlingman DJ, Mack AH, Kamenetska M, Mochrie SGJ, Regan L. Routes to DNA accessibility: alternative pathways for nucleosome unwinding. Biophys J 2015; 107:384-392. [PMID: 25028880 DOI: 10.1016/j.bpj.2014.05.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 04/02/2014] [Accepted: 05/23/2014] [Indexed: 01/01/2023] Open
Abstract
The dynamic packaging of DNA into chromatin is a key determinant of eukaryotic gene regulation and epigenetic inheritance. Nucleosomes are the basic unit of chromatin, and therefore the accessible states of the nucleosome must be the starting point for mechanistic models regarding these essential processes. Although the existence of different unwound nucleosome states has been hypothesized, there have been few studies of these states. The consequences of multiple states are far reaching. These states will behave differently in all aspects, including their interactions with chromatin remodelers, histone variant exchange, and kinetic properties. Here, we demonstrate the existence of two distinct states of the unwound nucleosome, which are accessible at physiological forces and ionic strengths. Using optical tweezers, we measure the rates of unwinding and rewinding for these two states and show that the rewinding rates from each state are different. In addition, we show that the probability of unwinding into each state is dependent on the applied force and ionic strength. Our results demonstrate not only that multiple unwound states exist but that their accessibility can be differentially perturbed, suggesting possible roles for these states in gene regulation. For example, different histone variants or modifications may facilitate or suppress access to DNA by promoting unwinding into one state or the other. We anticipate that the two unwound states reported here will be the basis for future models of eukaryotic transcriptional control.
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Affiliation(s)
- Daniel J Schlingman
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Andrew H Mack
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Applied Physics, Yale University, New Haven, Connecticut
| | - Masha Kamenetska
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut; Department of Physics, Yale University, New Haven, Connecticut
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Applied Physics, Yale University, New Haven, Connecticut; Department of Physics, Yale University, New Haven, Connecticut
| | - Lynne Regan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut; Department of Chemistry, Yale University, New Haven, Connecticut.
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41
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Inner Kinetochore Protein Interactions with Regional Centromeres of Fission Yeast. Genetics 2015; 201:543-61. [PMID: 26275423 PMCID: PMC4596668 DOI: 10.1534/genetics.115.179788] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/10/2015] [Indexed: 01/19/2023] Open
Abstract
Centromeres of the fission yeast Schizosaccharomyces pombe lack the highly repetitive sequences that make most other "regional" centromeres refractory to analysis. To map fission yeast centromeres, we applied H4S47C-anchored cleavage mapping and native and cross-linked chromatin immunoprecipitation with paired-end sequencing. H3 nucleosomes are nearly absent from the central domain, which is occupied by centromere-specific H3 (cenH3 or CENP-A) nucleosomes with two H4s per particle that are mostly unpositioned and are more widely spaced than nucleosomes elsewhere. Inner kinetochore proteins CENP-A, CENP-C, CENP-T, CENP-I, and Scm3 are highly enriched throughout the central domain except at tRNA genes, with no evidence for preferred kinetochore assembly sites. These proteins are weakly enriched and less stably incorporated in H3-rich heterochromatin. CENP-A nucleosomes protect less DNA from nuclease digestion than H3 nucleosomes, while CENP-T protects a range of fragment sizes. Our results suggest that CENP-T particles occupy linkers between CENP-A nucleosomes and that classical regional centromeres differ from other centromeres by the absence of CENP-A nucleosome positioning.
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Abstract
Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism.
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Affiliation(s)
- Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
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43
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Henikoff S. The Genetic Map Enters Its Second Century. Genetics 2015; 200:671-4. [PMID: 26170439 PMCID: PMC4512531 DOI: 10.1534/genetics.115.178434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Genetics Society of America (GSA) Medal is awarded to an individual for outstanding contributions to the field of genetics in the past 15 years. Recipients of the GSA Medal are recognized for elegant and highly meaningful contributions to modern genetics and exemplify the ingenuity of GSA members. The 2015 recipient is Steven Henikoff, whose achievements include major contributions to Drosophila genetics and epigenetics, Arabidopsis genetics and epigenetics, population and evolutionary genetics, genomic technologies, computational biology, and transcription and chromatin biology. Among these achievements, Henikoff elucidated the mechanism for position-effect variegation, revealed a central role for variant histones in nucleosome assembly at active genes, and provided new insights into genome evolution. He has also developed widely used computational tools for genome and protein analysis and new strategies for mapping chromatin-binding sites.
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Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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Steiner FA, Henikoff S. Diversity in the organization of centromeric chromatin. Curr Opin Genet Dev 2015; 31:28-35. [PMID: 25956076 DOI: 10.1016/j.gde.2015.03.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 03/26/2015] [Accepted: 03/28/2015] [Indexed: 01/15/2023]
Abstract
Centromeric chromatin is distinguished primarily by nucleosomes containing the histone variant cenH3, which organizes the kinetochore that links the chromosome to the spindle apparatus. Whereas budding yeast have simple 'point' centromeres with single cenH3 nucleosomes, and fission yeast have 'regional' centromeres without obvious sequence specificity, the centromeres of most organisms are embedded in highly repetitive 'satellite' DNA. Recent studies have revealed a remarkable diversity in centromere chromatin organization among different lineages, including some that have lost cenH3 altogether. We review recent progress in understanding point, regional and satellite centromeres, as well as less well-studied centromere types, such as holocentromeres. We also discuss the formation of neocentromeres, the role of pericentric heterochromatin, and the structure and composition of the cenH3 nucleosome.
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Affiliation(s)
- Florian A Steiner
- Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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45
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Fujita R, Otake K, Arimura Y, Horikoshi N, Miya Y, Shiga T, Osakabe A, Tachiwana H, Ohzeki JI, Larionov V, Masumoto H, Kurumizaka H. Stable complex formation of CENP-B with the CENP-A nucleosome. Nucleic Acids Res 2015; 43:4909-22. [PMID: 25916850 PMCID: PMC4446444 DOI: 10.1093/nar/gkv405] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 04/15/2015] [Indexed: 01/16/2023] Open
Abstract
CENP-A and CENP-B are major components of centromeric chromatin. CENP-A is the histone H3 variant, which forms the centromere-specific nucleosome. CENP-B specifically binds to the CENP-B box DNA sequence on the centromere-specific repetitive DNA. In the present study, we found that the CENP-A nucleosome more stably retains human CENP-B than the H3.1 nucleosome in vitro. Specifically, CENP-B forms a stable complex with the CENP-A nucleosome, when the CENP-B box sequence is located at the proximal edge of the nucleosome. Surprisingly, the CENP-B binding was weaker when the CENP-B box sequence was located in the distal linker region of the nucleosome. This difference in CENP-B binding, depending on the CENP-B box location, was not observed with the H3.1 nucleosome. Consistently, we found that the DNA-binding domain of CENP-B specifically interacted with the CENP-A-H4 complex, but not with the H3.1-H4 complex, in vitro. These results suggested that CENP-B forms a more stable complex with the CENP-A nucleosome through specific interactions with CENP-A, if the CENP-B box is located proximal to the CENP-A nucleosome. Our in vivo assay also revealed that CENP-B binding in the vicinity of the CENP-A nucleosome substantially stabilizes the CENP-A nucleosome on alphoid DNA in human cells.
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Affiliation(s)
- Risa Fujita
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Koichiro Otake
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yasuhiro Arimura
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Naoki Horikoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yuta Miya
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Tatsuya Shiga
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Jun-ichirou Ohzeki
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Vladimir Larionov
- Development Therapeutic Branch, National Cancer Institute, National Institutes of Health, Building 37, Room 5040, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Hiroshi Masumoto
- Laboratory of Cell Engineering, Department of Frontier Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - 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
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46
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Li G, Zhu P. Structure and organization of chromatin fiber in the nucleus. FEBS Lett 2015; 589:2893-904. [PMID: 25913782 DOI: 10.1016/j.febslet.2015.04.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 12/30/2022]
Abstract
Eukaryotic genomes are organized hierarchically into chromatin structures by histones. Despite extensive research for over 30 years, not only the fundamental structure of the 30-nm chromatin fiber is being debated, but the actual existence of such fiber remains hotly contested. In this review, we focus on the most recent progress in elucidating the structure of the 30-nm fiber upon in vitro reconstitution, and its possible organization inside the nucleus. In addition, we discuss the roles of linker histone H1 as well as the importance of specific nucleosome-nucleosome interactions in the formation of the 30-nm fiber. Finally, we discuss the involvement of structural variations and epigenetic mechanisms available for the regulation of this chromatin form.
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Affiliation(s)
- Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ping Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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47
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Abendroth C, Hofmeister A, Hake SB, Kamweru PK, Miess E, Dornblut C, Küffner I, Deng W, Leonhardt H, Orthaus S, Hoischen C, Diekmann S. The CENP-T C-terminus is exclusively proximal to H3.1 and not to H3.2 or H3.3. Int J Mol Sci 2015; 16:5839-63. [PMID: 25775162 PMCID: PMC4394509 DOI: 10.3390/ijms16035839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/18/2015] [Accepted: 02/18/2015] [Indexed: 12/17/2022] Open
Abstract
The kinetochore proteins assemble onto centromeric chromatin and regulate DNA segregation during cell division. The inner kinetochore proteins bind centromeres while most outer kinetochore proteins assemble at centromeres during mitosis, connecting the complex to microtubules. The centromere-kinetochore complex contains specific nucleosomes and nucleosomal particles. CENP-A replaces canonical H3 in centromeric nucleosomes, defining centromeric chromatin. Next to CENP-A, the CCAN multi-protein complex settles which contains CENP-T/W/S/X. These four proteins are described to form a nucleosomal particle at centromeres. We had found the CENP-T C-terminus and the CENP-S termini next to histone H3.1 but not to CENP-A, suggesting that the Constitutive Centromere-Associated Network (CCAN) bridges a CENP-A- and a H3-containing nucleosome. Here, we show by in vivo FRET that this proximity between CENP-T and H3 is specific for H3.1 but neither for the H3.1 mutants H3.1(C96A) and H3.1(C110A) nor for H3.2 or H3.3. We also found CENP-M next to H3.1 but not to these H3.1 mutants. Consistently, we detected CENP-M next to CENP-S. These data elucidate the local molecular neighborhood of CCAN proteins next to a H3.1-containing centromeric nucleosome. They also indicate an exclusive position of H3.1 clearly distinct from H3.2, thus documenting a local, and potentially also functional, difference between H3.1 and H3.2.
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Affiliation(s)
- Christian Abendroth
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Antje Hofmeister
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Sandra B Hake
- Department of Molecular Biology, Center for Integrated Protein Science Munich (CIPSM), Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität Munich, Schillerstr. 44, D-80336 Munich, Germany.
| | - Paul K Kamweru
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Elke Miess
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Carsten Dornblut
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Isabell Küffner
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Wen Deng
- Department of Biology II, Center for Integrated Protein Science, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, D-82152 Munich, Germany.
| | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, D-82152 Munich, Germany.
| | | | - Christian Hoischen
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
| | - Stephan Diekmann
- Molecular Biology, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany.
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48
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Athwal RK, Walkiewicz MP, Baek S, Fu S, Bui M, Camps J, Ried T, Sung MH, Dalal Y. CENP-A nucleosomes localize to transcription factor hotspots and subtelomeric sites in human cancer cells. Epigenetics Chromatin 2015; 8:2. [PMID: 25788983 PMCID: PMC4363203 DOI: 10.1186/1756-8935-8-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022] Open
Abstract
Background The histone H3 variant CENP-A is normally tightly regulated to ensure only one centromere exists per chromosome. Native CENP-A is often found overexpressed in human cancer cells and a range of human tumors. Consequently, CENP-A misregulation is thought to contribute to genome instability in human cancers. However, the consequences of such overexpression have not been directly elucidated in human cancer cells. Results To investigate native CENP-A overexpression, we sought to uncover CENP-A-associated defects in human cells. We confirm that CENP-A is innately overexpressed in several colorectal cancer cell lines. In such cells, we report that a subset of structurally distinct CENP-A-containing nucleosomes associate with canonical histone H3, and with the transcription-coupled chaperones ATRX and DAXX. Furthermore, such hybrid CENP-A nucleosomes localize to DNase I hypersensitive and transcription factor binding sites, including at promoters of genes across the human genome. A distinct class of CENP-A hotspots also accumulates at subtelomeric chromosomal locations, including at the 8q24/Myc region long-associated with genomic instability. We show this 8q24 accumulation of CENP-A can also be seen in early stage primary colorectal tumors. Conclusions Our data demonstrate that excess CENP-A accumulates at noncentromeric locations in the human cancer genome. These findings suggest that ectopic CENP-A nucleosomes could alter the state of the chromatin fiber, potentially impacting gene regulation and chromosome fragility. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-8-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rajbir K Athwal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Marcin P Walkiewicz
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Song Fu
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Minh Bui
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Jordi Camps
- Genetics Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health, 50 South Drive, Bethesda, MD 20892 USA
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health, 50 South Drive, Bethesda, MD 20892 USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Yamini Dalal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
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Abstract
Histones package and compact DNA by assembling into nucleosome core particles. Most histones are synthesized at S phase for rapid deposition behind replication forks. In addition, the replacement of histones deposited during S phase by variants that can be deposited independently of replication provide the most fundamental level of chromatin differentiation. Alternative mechanisms for depositing different variants can potentially establish and maintain epigenetic states. Variants have also evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, and other processes. Investigations into the evolution, structure, and metabolism of histone variants provide a foundation for understanding the participation of chromatin in important cellular processes and in epigenetic memory.
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Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024
| | - M Mitchell Smith
- Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908
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50
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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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