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Bui M, Baek S, Bentahar RS, Melters DP, Dalal Y. Native and tagged CENP-A histones are functionally inequivalent. Epigenetics Chromatin 2024; 17:19. [PMID: 38825690 PMCID: PMC11145777 DOI: 10.1186/s13072-024-00543-9] [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: 02/07/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Over the past several decades, the use of biochemical and fluorescent tags has elucidated mechanistic and cytological processes that would otherwise be impossible. The challenging nature of certain nuclear proteins includes low abundancy, poor antibody recognition, and transient dynamics. One approach to get around those issues is the addition of a peptide or larger protein tag to the target protein to improve enrichment, purification, and visualization. However, many of these studies were done under the assumption that tagged proteins can fully recapitulate native protein function. RESULTS We report that when C-terminally TAP-tagged CENP-A histone variant is introduced, it undergoes altered kinetochore protein binding, differs in post-translational modifications (PTMs), utilizes histone chaperones that differ from that of native CENP-A, and can partially displace native CENP-A in human cells. Additionally, these tagged CENP-A-containing nucleosomes have reduced centromeric incorporation at early G1 phase and poorly associates with linker histone H1.5 compared to native CENP-A nucleosomes. CONCLUSIONS These data suggest expressing tagged versions of histone variant CENP-A may result in unexpected utilization of non-native pathways, thereby altering the biological function of the histone variant.
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Affiliation(s)
- Minh Bui
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA.
| | - Songjoon Baek
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Reda S Bentahar
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Daniël P Melters
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Yamini Dalal
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA.
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2
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Rakshit T, Melters DP, Dimitriadis EK, Dalal Y. Mechanical properties of nucleoprotein complexes determined by nanoindentation spectroscopy. Nucleus 2021; 11:264-282. [PMID: 32954931 PMCID: PMC7529419 DOI: 10.1080/19491034.2020.1816053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The interplay between transcription factors, chromatin remodelers, 3-D organization, and mechanical properties of the chromatin fiber controls genome function in eukaryotes. Besides the canonical histones which fold the bulk of the chromatin into nucleosomes, histone variants create distinctive chromatin domains that are thought to regulate transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether histone variants translate distinctive biochemical or biophysical properties to their associated chromatin structures, and whether these properties impact chromatin dynamics as the genome undergoes a multitude of transactions, is an important question in biology. Here, we describe single-molecule nanoindentation tools that we developed specifically to determine the mechanical properties of histone variant nucleosomes and their complexes. These methods join an array of cutting-edge new methods that further our quantitative understanding of the response of chromatin to intrinsic and extrinsic forces which act upon it during biological transactions in the nucleus.
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Affiliation(s)
- Tatini Rakshit
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA.,Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Salt Lake, India
| | - Daniël P Melters
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Emilios K Dimitriadis
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
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3
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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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4
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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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5
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Melters DP, Pitman M, Rakshit T, Dimitriadis EK, Bui M, Papoian GA, Dalal Y. Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners. Proc Natl Acad Sci U S A 2019; 116:24066-24074. [PMID: 31712435 PMCID: PMC6883791 DOI: 10.1073/pnas.1911880116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Histone variants fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether and how nucleosome variants encode unique mechanical properties to their cognate chromatin structures remains elusive. Here, using in silico and in vitro nanoindentation methods, extending to in vivo dissections, we report that histone variant nucleosomes are intrinsically more elastic than their canonical counterparts. Furthermore, binding proteins, which discriminate between histone variant nucleosomes, suppress this innate elasticity and also compact chromatin. Interestingly, when we overexpress the binding proteins in vivo, we also observe increased compaction of chromatin enriched for histone variant nucleosomes, correlating with diminished access. Taken together, these data suggest a plausible link between innate mechanical properties possessed by histone variant nucleosomes, the adaptability of chromatin states in vivo, and the epigenetic plasticity of the underlying locus.
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Affiliation(s)
- Daniël P Melters
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Mary Pitman
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742
| | - Tatini Rakshit
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Emilios K Dimitriadis
- Scanning Probe Microscopy Unit, Biomedical Engineering and Physical Science Shared Resource, National Institute for Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Minh Bui
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Garegin A Papoian
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742;
| | - Yamini Dalal
- Laboratory Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892;
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6
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Lyubchenko YL. Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:403001. [PMID: 30410191 PMCID: PMC6217977 DOI: 10.1088/1361-6463/aad898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
High-speed AFM (HS-AFM) is an advanced technique with numerous applications in biology, particularly in molecular biophysics. Developed as a time-lapse AFM technique for direct imaging fully hydrated biological molecules, HS-AFM is currently capable of visualizing the dynamics of biological molecules and their complexes at a video-data acquisition rate. Spatial resolution at the nanometer level is another important characteristic of HS-AFM. This review focuses on examples of primarily protein-DNA complexes to illustrate the high temporal and spatial resolution capabilities of HS-AFM that have resulted in novel models and/or the functional mechanisms of these biological systems.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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7
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Vlijm R, Kim SH, De Zwart PL, Dalal Y, Dekker C. The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes. NANOSCALE 2017; 9:1862-1870. [PMID: 28094382 PMCID: PMC7959483 DOI: 10.1039/c6nr06245h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness of the DNA wrapping around the nucleosome core is intrinsically ambidextrous, and depends on the pre-assembly supercoiling state of the DNA, i.e., it is not uniquely determined by the octameric histone core. Nucleosomes assembled onto negatively supercoiled DNA are found to exhibit a left-handed conformation, whereas assembly onto positively supercoiled DNA results in right-handed nucleosomes. This intrinsic flexibility to adopt both chiralities is observed both for canonical H3 nucleosomes, and for centromere-specific variant CENP-A nucleosomes. These data support recent advances suggesting an intrinsic adaptability of the nucleosome, and provide insights into how nucleosomes might rapidly re-assemble after cellular processes that generate positive supercoiling in vivo.
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Affiliation(s)
- R Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - S H Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - P L De Zwart
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - Y Dalal
- Chromatin Structure and Epigenetic Mechanisms Unit, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - C Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
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8
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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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9
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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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10
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Melters DP, Nye J, Zhao H, Dalal Y. Chromatin Dynamics in Vivo: A Game of Musical Chairs. Genes (Basel) 2015; 6:751-76. [PMID: 26262644 PMCID: PMC4584328 DOI: 10.3390/genes6030751] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/17/2015] [Accepted: 07/28/2015] [Indexed: 01/30/2023] Open
Abstract
Histones are a major component of chromatin, the nucleoprotein complex fundamental to regulating transcription, facilitating cell division, and maintaining genome integrity in almost all eukaryotes. In addition to canonical, replication-dependent histones, replication-independent histone variants exist in most eukaryotes. In recent years, steady progress has been made in understanding how histone variants assemble, their involvement in development, mitosis, transcription, and genome repair. In this review, we will focus on the localization of the major histone variants H3.3, CENP-A, H2A.Z, and macroH2A, as well as how these variants have evolved, their structural differences, and their functional significance in vivo.
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Affiliation(s)
- Daniël P Melters
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Jonathan Nye
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
| | - Haiqing Zhao
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA.
| | - Yamini Dalal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD 20892, USA.
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11
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Fang J, Liu Y, Wei Y, Deng W, Yu Z, Huang L, Teng Y, Yao T, You Q, Ruan H, Chen P, Xu RM, Li G. Structural transitions of centromeric chromatin regulate the cell cycle-dependent recruitment of CENP-N. Genes Dev 2015; 29:1058-73. [PMID: 25943375 PMCID: PMC4441053 DOI: 10.1101/gad.259432.115] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/13/2015] [Indexed: 11/24/2022]
Abstract
Specific recognition of centromere-specific histone variant CENP-A-containing chromatin by CENP-N is an essential process in the assembly of the kinetochore complex at centromeres prior to mammalian cell division. However, the mechanisms of CENP-N recruitment to centromeres/kinetochores remain unknown. Here, we show that a CENP-A-specific RG loop (Arg80/Gly81) plays an essential and dual regulatory role in this process. The RG loop assists the formation of a compact "ladder-like" structure of CENP-A chromatin, concealing the loop and thus impairing its role in recruiting CENP-N. Upon G1/S-phase transition, however, centromeric chromatin switches from the compact to an open state, enabling the now exposed RG loop to recruit CENP-N prior to cell division. Our results provide the first insights into the mechanisms by which the recruitment of CENP-N is regulated by the structural transitions between compaction and relaxation of centromeric chromatin during the cell cycle.
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Affiliation(s)
- Junnan Fang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuting Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wei
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenqiang Deng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhouliang Yu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Teng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Yao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinglong You
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haihe Ruan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ping Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
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12
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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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13
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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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Biterge B, Schneider R. Histone variants: key players of chromatin. Cell Tissue Res 2014; 356:457-66. [PMID: 24781148 DOI: 10.1007/s00441-014-1862-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 02/27/2014] [Indexed: 01/01/2023]
Abstract
Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.
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Affiliation(s)
- Burcu Biterge
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, 67404, Illkirch, France
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Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang JP, Henikoff JG. The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. eLife 2014; 3:e01861. [PMID: 24737863 PMCID: PMC3983907 DOI: 10.7554/elife.01861] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In budding yeast, a single cenH3 (Cse4) nucleosome occupies the ∼120-bp functional centromere, however conflicting structural models for the particle have been proposed. To resolve this controversy, we have applied H4S47C-anchored cleavage mapping, which reveals the precise position of histone H4 in every nucleosome in the genome. We find that cleavage patterns at centromeres are unique within the genome and are incompatible with symmetrical structures, including octameric nucleosomes and (Cse4/H4)2 tetrasomes. Centromere cleavage patterns are compatible with a precisely positioned core structure, one in which each of the 16 yeast centromeres is occupied by oppositely oriented Cse4/H4/H2A/H2B hemisomes in two rotational phases within the population. Centromere-specific hemisomes are also inferred from distances observed between closely-spaced H4 cleavages, as predicted from structural modeling. Our results indicate that the orientation and rotational position of the stable hemisome at each yeast centromere is not specified by the functional centromere sequence. DOI:http://dx.doi.org/10.7554/eLife.01861.001 DNA is tightly packaged in cells for a variety of reasons—to allow it to fit inside the nucleus, to protect it from damage, and to help control the production of proteins from genes. The basic unit of packaged DNA is called a nucleosome, which consists of DNA wrapped around a structure formed by two pairs of four different proteins. These proteins, which are called histones, have a role that extends beyond providing structural support for DNA. When cells divide, for example, pairs of ‘sister chromosomes’ are pulled apart to ensure that the two daughter cells both have the same chromosomes as the original cell. The sister chromosomes are pulled apart from a single position called a centromere, and the nucleosomes at this position contain a histone that is different from the histones found everywhere else in the cell. However, until recently it was not clear if the nucleosomes that contained these special cenH3 histones had the same structure as other nucleosomes. Now Henikoff et al. have used a method called H4S47C-anchored cleavage mapping to study every nucleosome in the genome of the yeast S. cerevisiae. This mapping technique uses DNA sequencing to measure the precise distances between fixed points on the DNA in the nucleosome. Knowing these distances tells researchers a great deal about the number and position of the histones within each nucleosome in the genome. Using this approach, Henikoff et al. found that nucleosomes at centromeres are different from other nucleosomes in histone number and arrangement. In particular, the nucleosome at each yeast centromere contains only one each of the four different histones in an asymmetrical orientation, in contrast to all other yeast nucleosomes, which contain two sets of four histones in a symmetrical arrangement. Furthermore, each nucleosome at a centromere can adopt one of two orientations: these orientations are mirror images of each other, and they occur with equal probability. It should also be possible to use the mapping technique developed by Henikoff et al. to study the larger and more complex centromeres found in other organisms, including humans. DOI:http://dx.doi.org/10.7554/eLife.01861.002
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Affiliation(s)
- Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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Reply to "CENP-A octamers do not confer a reduction in nucleosome height by AFM". Nat Struct Mol Biol 2014; 21:5-8. [PMID: 24389543 DOI: 10.1038/nsmb.2744] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Volle C, Dalal Y. Histone variants: the tricksters of the chromatin world. Curr Opin Genet Dev 2014; 25:8-14,138. [PMID: 24463272 DOI: 10.1016/j.gde.2013.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 11/05/2013] [Indexed: 12/26/2022]
Abstract
The eukaryotic genome exists in vivo at an equimolar ratio with histones, thus forming a polymer composed of DNA and histone proteins. Each nucleosomal unit in this polymer provides versatile capabilities and dynamic range. Substitutions of the individual components of the histone core with structurally distinct histone variants and covalent modifications alter the local fabric of the chromatin fiber, resulting in epigenetic changes that can be regulated by the cell. In this review, we highlight recent advances in the study of histone variant structure, assembly, and inheritance, their influence on nucleosome positioning, and their cumulative effect upon gene expression, DNA repair and the progression of disease. We also highlight fundamental questions that remain unanswered regarding the behavior of histone variants and their influence on cellular function in the normal and diseased states.
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Affiliation(s)
- Catherine Volle
- Chromatin Structure and Epigenetic Mechanisms Team, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yamini Dalal
- Chromatin Structure and Epigenetic Mechanisms Team, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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