1
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Lin YY, Müller P, Karagianni E, Hepp N, Mueller-Planitz F, Vanderlinden W, Lipfert J. Epigenetic Histone Modifications H3K36me3 and H4K5/8/12/16ac Induce Open Polynucleosome Conformations via Different Mechanisms. J Mol Biol 2024; 436:168671. [PMID: 38908785 DOI: 10.1016/j.jmb.2024.168671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/28/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Nucleosomes are the basic compaction unit of chromatin and nucleosome structure and their higher-order assemblies regulate genome accessibility. Many post-translational modifications alter nucleosome dynamics, nucleosome-nucleosome interactions, and ultimately chromatin structure and gene expression. Here, we investigate the role of two post-translational modifications associated with actively transcribed regions, H3K36me3 and H4K5/8/12/16ac, in the contexts of tri-nucleosome arrays that provide a tractable model system for quantitative single-molecule analysis, while enabling us to probe nucleosome-nucleosome interactions. Direct visualization by AFM imaging reveals that H3K36me3 and H4K5/8/12/16ac nucleosomes adopt significantly more open and loose conformations than unmodified nucleosomes. Similarly, magnetic tweezers force spectroscopy shows a reduction in DNA outer turn wrapping and nucleosome-nucleosome interactions for the modified nucleosomes. The results suggest that for H3K36me3 the increased breathing and outer DNA turn unwrapping seen in mononucleosomes propagates to more open conformations in nucleosome arrays. In contrast, the even more open structures of H4K5/8/12/16ac nucleosome arrays do not appear to derive from the dynamics of the constituent mononucleosomes, but are driven by reduced nucleosome-nucleosome interactions, suggesting that stacking interactions can overrule DNA breathing of individual nucleosomes. We anticipate that our methodology will be broadly applicable to reveal the influence of other post-translational modifications and to observe the activity of nucleosome remodelers.
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Affiliation(s)
- Yi-Yun Lin
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands
| | - Peter Müller
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands
| | - Evdoxia Karagianni
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands
| | - Nicola Hepp
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany; Current address: Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands; School of Physics and Astronomy, University of Edinburg, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.
| | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands.
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2
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Prescott NA, Mansisidor A, Bram Y, Biaco T, Rendleman J, Faulkner SC, Lemmon AA, Lim C, Hamard PJ, Koche RP, Risca VI, Schwartz RE, David Y. A nucleosome switch primes Hepatitis B Virus infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.03.531011. [PMID: 38915612 PMCID: PMC11195122 DOI: 10.1101/2023.03.03.531011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Chronic hepatitis B virus (HBV) infection is an incurable global health threat responsible for causing liver disease and hepatocellular carcinoma. During the genesis of infection, HBV establishes an independent minichromosome consisting of the viral covalently closed circular DNA (cccDNA) genome and host histones. The viral X gene must be expressed immediately upon infection to induce degradation of the host silencing factor, Smc5/6. However, the relationship between cccDNA chromatinization and X gene transcription remains poorly understood. Establishing a reconstituted viral minichromosome platform, we found that nucleosome occupancy in cccDNA drives X transcription. We corroborated these findings in cells and further showed that the chromatin destabilizing molecule CBL137 inhibits X transcription and HBV infection in hepatocytes. Our results shed light on a long-standing paradox and represent a potential new therapeutic avenue for the treatment of chronic HBV infection.
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Affiliation(s)
- Nicholas A. Prescott
- Tri-Institutional PhD Program in Chemical Biology; New York, NY 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Andrés Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University; New York, NY 10065, USA
- These authors contributed equally
| | - Yaron Bram
- Division of Gastroenterology & Hepatology, Department of Medicine, Weill Cornell Medicine; New York, NY 10065, USA
- These authors contributed equally
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Department of Pharmacology, Weill Cornell Medicine; New York, NY 10065, USA
- These authors contributed equally
| | - Justin Rendleman
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University; New York, NY 10065, USA
| | - Sarah C. Faulkner
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Abigail A. Lemmon
- Tri-Institutional PhD Program in Chemical Biology; New York, NY 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Christine Lim
- Division of Gastroenterology & Hepatology, Department of Medicine, Weill Cornell Medicine; New York, NY 10065, USA
| | - Pierre-Jacques Hamard
- Epigenetics Research Innovation Lab, Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Richard P. Koche
- Epigenetics Research Innovation Lab, Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University; New York, NY 10065, USA
| | - Robert E. Schwartz
- Division of Gastroenterology & Hepatology, Department of Medicine, Weill Cornell Medicine; New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine; New York, NY 10065, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology; New York, NY 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center; New York, NY 10065, USA
- Department of Pharmacology, Weill Cornell Medicine; New York, NY 10065, USA
- Lead Contact
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3
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Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.575103. [PMID: 38352334 PMCID: PMC10862743 DOI: 10.1101/2024.01.29.575103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Regulation of histone proteins affects gene expression through multiple mechanisms including exchange with histone variants. However, widely expressed variants of H2B remain elusive. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. We applied new tools including novel antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE, and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Lastly, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a novel mechanism linking histone variants to chromatin regulation, neuronal function, and memory. This work further identifies the first widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
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Affiliation(s)
- Emily R. Feierman
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine C. Palozola
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Anna J. Voss
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Shreya D. Mehta
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Camille N. Quaye
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine T. Lynch
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Marc V. Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Erica Korb
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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4
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Câmara AS, Kubalová I, Schubert V. Helical chromonema coiling is conserved in eukaryotes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1284-1300. [PMID: 37840457 DOI: 10.1111/tpj.16484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023]
Abstract
Efficient chromatin condensation is required to transport chromosomes during mitosis and meiosis, forming daughter cells. While it is well accepted that these processes follow fundamental rules, there has been a controversial debate for more than 140 years on whether the higher-order chromatin organization in chromosomes is evolutionarily conserved. Here, we summarize historical and recent investigations based on classical and modern methods. In particular, classical light microscopy observations based on living, fixed, and treated chromosomes covering a wide range of plant and animal species, and even in single-cell eukaryotes suggest that the chromatids of large chromosomes are formed by a coiled chromatin thread, named the chromonema. More recently, these findings were confirmed by electron and super-resolution microscopy, oligo-FISH, molecular interaction data, and polymer simulation. Altogether, we describe common and divergent features of coiled chromonemata in different species. We hypothesize that chromonema coiling in large chromosomes is a fundamental feature established early during the evolution of eukaryotes to handle increasing genome sizes.
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Affiliation(s)
- Amanda Souza Câmara
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Ivona Kubalová
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466, Seeland, Germany
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5
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Abasi LS, Elathram N, Movva M, Deep A, Corbett KD, Debelouchina GT. Phosphorylation regulates tau's phase separation behavior and interactions with chromatin. Commun Biol 2024; 7:251. [PMID: 38429335 PMCID: PMC10907630 DOI: 10.1038/s42003-024-05920-4] [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: 12/21/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
Tau is a microtubule-associated protein often found in neurofibrillary tangles (NFTs) in the brains of patients with Alzheimer's disease. Beyond this context, mounting evidence suggests that tau localizes into the nucleus, where it may play a role in DNA protection and heterochromatin regulation. The molecular mechanisms behind these observations are currently unclear. Using in vitro biophysical experiments, here we demonstrate that tau can undergo liquid-liquid phase separation (LLPS) with DNA, mononucleosomes, and reconstituted nucleosome arrays under low salt conditions. Low concentrations of tau promote chromatin compaction and protect DNA from digestion. While the material state of samples at physiological salt is dominated by chromatin oligomerization, tau can still associate strongly and reversibly with nucleosome arrays. These properties are driven by tau's strong interactions with linker and nucleosomal DNA. In addition, tau co-localizes into droplets formed by nucleosome arrays and phosphorylated HP1α, a key heterochromatin constituent thought to function through an LLPS mechanism. Importantly, LLPS and chromatin interactions are disrupted by aberrant tau hyperphosphorylation. These biophysical properties suggest that tau may directly impact DNA and chromatin accessibility and that loss of these interactions could contribute to the aberrant nuclear effects seen in tau pathology.
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Affiliation(s)
- Lannah S Abasi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Manasi Movva
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Galia T Debelouchina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
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6
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Lin X, Zhang B. Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 2024; 12:RP90073. [PMID: 38289342 PMCID: PMC10945522 DOI: 10.7554/elife.90073] [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] [Indexed: 09/01/2023] Open
Abstract
Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 kBT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono- and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9 kBT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
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7
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Abasi LS, Elathram N, Movva M, Deep A, Corbett KD, Debelouchina GT. Phosphorylation regulates tau's phase separation behavior and interactions with chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572911. [PMID: 38187700 PMCID: PMC10769318 DOI: 10.1101/2023.12.21.572911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Tau is a microtubule-associated protein often found in neurofibrillary tangles (NFTs) in the brains of patients with Alzheimer's disease (AD). Beyond this context, mounting evidence suggests that tau localizes into the nucleus, where it may play a role in DNA protection and heterochromatin regulation. Models of tau depletion or pathology show loss of genetically silent heterochromatin, aberrant expression of heterochromatic genes, and transposable element activation. The molecular mechanisms behind these observations are currently unclear. Using in vitro biophysical experiments, here we demonstrate that tau can undergo liquid-liquid phase separation (LLPS) with DNA, mononucleosomes, and reconstituted nucleosome arrays under low salt conditions. Low concentrations of tau promote chromatin compaction and protect DNA from digestion. While the material state of samples at physiological salt is dominated by chromatin oligomerization, tau can still associate strongly and reversibly with nucleosome arrays. These properties are driven by tau's strong interactions with linker and nucleosomal DNA, while magic angle spinning (MAS) solid-state NMR experiments show that tau binding does not drastically alter nucleosome structure and dynamics. In addition, tau co-localizes into droplets formed by nucleosome arrays and phosphorylated HP1α, a key heterochromatin constituent thought to function through an LLPS mechanism. Importantly, LLPS and chromatin interactions are disrupted by aberrant tau hyperphosphorylation. These biophysical properties suggest that tau may directly impact DNA and chromatin accessibility and that loss of these interactions could contribute to the aberrant nuclear effects seen in tau pathology.
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Affiliation(s)
- Lannah S. Abasi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Manasi Movva
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin D. Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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8
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Lin X, Zhang B. Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541030. [PMID: 37293007 PMCID: PMC10245791 DOI: 10.1101/2023.05.16.541030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 kBT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9 kBT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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9
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Oleinikov PD, Fedulova AS, Armeev GA, Motorin NA, Singh-Palchevskaia L, Sivkina AL, Feskin PG, Glukhov GS, Afonin DA, Komarova GA, Kirpichnikov MP, Studitsky VM, Feofanov AV, Shaytan AK. Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study. Int J Mol Sci 2023; 24:15194. [PMID: 37894874 PMCID: PMC10606924 DOI: 10.3390/ijms242015194] [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: 09/25/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
In eukaryotic organisms, genomic DNA associates with histone proteins to form nucleosomes. Nucleosomes provide a basis for genome compaction, epigenetic markup, and mediate interactions of nuclear proteins with their target DNA loci. A negatively charged (acidic) patch located on the H2A-H2B histone dimer is a characteristic feature of the nucleosomal surface. The acidic patch is a common site in the attachment of various chromatin proteins, including viral ones. Acidic patch-binding peptides present perspective compounds that can be used to modulate chromatin functioning by disrupting interactions of nucleosomes with natural proteins or alternatively targeting artificial moieties to the nucleosomes, which may be beneficial for the development of new therapeutics. In this work, we used several computational and experimental techniques to improve our understanding of how peptides may bind to the acidic patch and what are the consequences of their binding. Through extensive analysis of the PDB database, histone sequence analysis, and molecular dynamic simulations, we elucidated common binding patterns and key interactions that stabilize peptide-nucleosome complexes. Through MD simulations and FRET measurements, we characterized changes in nucleosome dynamics conferred by peptide binding. Using fluorescence polarization and gel electrophoresis, we evaluated the affinity and specificity of the LANA1-22 peptide to DNA and nucleosomes. Taken together, our study provides new insights into the different patterns of intermolecular interactions that can be employed by natural and designed peptides to bind to nucleosomes, and the effects of peptide binding on nucleosome dynamics and stability.
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Affiliation(s)
- Pavel D. Oleinikov
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | | | - Grigoriy A. Armeev
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nikita A. Motorin
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | | | - Anastasiia L. Sivkina
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Laboratory of Structural-Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Pavel G. Feskin
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Grigory S. Glukhov
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen 518172, China
| | - Dmitry A. Afonin
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Galina A. Komarova
- Department of Physics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Vasily M. Studitsky
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Alexey V. Feofanov
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexey K. Shaytan
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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10
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Sahu S, Ekundayo BE, Kumar A, Bleichert F. A dual role for the chromatin reader ORCA/LRWD1 in targeting the origin recognition complex to chromatin. EMBO J 2023; 42:e114654. [PMID: 37551430 PMCID: PMC10505921 DOI: 10.15252/embj.2023114654] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/09/2023] Open
Abstract
Eukaryotic cells use chromatin marks to regulate the initiation of DNA replication. The origin recognition complex (ORC)-associated protein ORCA plays a critical role in heterochromatin replication in mammalian cells by recruiting the initiator ORC, but the underlying mechanisms remain unclear. Here, we report crystal and cryo-electron microscopy structures of ORCA in complex with ORC's Orc2 subunit and nucleosomes, establishing that ORCA orchestrates ternary complex assembly by simultaneously recognizing a highly conserved peptide sequence in Orc2, nucleosomal DNA, and repressive histone trimethylation marks through an aromatic cage. Unexpectedly, binding of ORCA to nucleosomes prevents chromatin array compaction in a manner that relies on H4K20 trimethylation, a histone modification critical for heterochromatin replication. We further show that ORCA is necessary and sufficient to specifically recruit ORC into chromatin condensates marked by H4K20 trimethylation, providing a paradigm for studying replication initiation in specific chromatin contexts. Collectively, our findings support a model in which ORCA not only serves as a platform for ORC recruitment to nucleosomes bearing specific histone marks but also helps establish a local chromatin environment conducive to subsequent MCM2-7 loading.
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Affiliation(s)
- Sumon Sahu
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
| | - Babatunde E Ekundayo
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
- Present address:
Laboratory of Biological Electron MicroscopyEPFLLausanneSwitzerland
| | - Ashish Kumar
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
| | - Franziska Bleichert
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
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11
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Chen Q, Zhao L, Soman A, Arkhipova AY, Li J, Li H, Chen Y, Shi X, Nordenskiöld L. Chromatin Liquid-Liquid Phase Separation (LLPS) Is Regulated by Ionic Conditions and Fiber Length. Cells 2022; 11:cells11193145. [PMID: 36231107 PMCID: PMC9564186 DOI: 10.3390/cells11193145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/20/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
The dynamic regulation of the physical states of chromatin in the cell nucleus is crucial for maintaining cellular homeostasis. Chromatin can exist in solid- or liquid-like forms depending on the surrounding ions, binding proteins, post-translational modifications and many other factors. Several recent studies suggested that chromatin undergoes liquid-liquid phase separation (LLPS) in vitro and also in vivo; yet, controversial conclusions about the nature of chromatin LLPS were also observed from the in vitro studies. These inconsistencies are partially due to deviations in the in vitro buffer conditions that induce the condensation/aggregation of chromatin as well as to differences in chromatin (nucleosome array) constructs used in the studies. In this work, we present a detailed characterization of the effects of K+, Mg2+ and nucleosome fiber length on the physical state and property of reconstituted nucleosome arrays. LLPS was generally observed for shorter nucleosome arrays (15-197-601, reconstituted from 15 repeats of the Widom 601 DNA with 197 bp nucleosome repeat length) at physiological ion concentrations. In contrast, gel- or solid-like condensates were detected for the considerably longer 62-202-601 and lambda DNA (~48.5 kbp) nucleosome arrays under the same conditions. In addition, we demonstrated that the presence of reduced BSA and acetate buffer is not essential for the chromatin LLPS process. Overall, this study provides a comprehensive understanding of several factors regarding chromatin physical states and sheds light on the mechanism and biological relevance of chromatin phase separation in vivo.
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Affiliation(s)
- Qinming Chen
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (Q.C.); (A.S.)
| | - Lei Zhao
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
| | - Aghil Soman
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (Q.C.); (A.S.)
| | - Anastasia Yu Arkhipova
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
- Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Jindi Li
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
| | - Hao Li
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
| | - Yinglu Chen
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
| | - Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China; (L.Z.); (A.Y.A.); (J.L.); (H.L.); (Y.C.)
- Correspondence: (X.S.); (L.N.)
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (Q.C.); (A.S.)
- Correspondence: (X.S.); (L.N.)
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12
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Hammonds EF, Harwig MC, Paintsil EA, Tillison EA, Hill RB, Morrison EA. Histone H3 and H4 tails play an important role in nucleosome phase separation. Biophys Chem 2022; 283:106767. [PMID: 35158124 PMCID: PMC8963862 DOI: 10.1016/j.bpc.2022.106767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022]
Abstract
Chromatin organization and its dynamic regulation are crucial in governing the temporal and spatial accessibility of DNA for proper gene expression. Disordered chains of nucleosomes comprise the basis of eukaryotic chromatin, forming higher-level organization across a range of length scales. Models of chromatin organization involving phase separation driven by chromatin-associating proteins have been proposed. More recently, evidence has emerged that nucleosome arrays can phase separate in the absence of other protein factors, yet questions remain regarding the molecular basis of chromatin phase separation that governs this dynamic nuclear organization. Here, we break chromatin down into its most basic subunit, the nucleosome core particle, and investigate phase separation using turbidity assays in conjunction with differential interference contrast microscopy. We show that, at physiologically-relevant concentrations, this fundamental subunit of chromatin undergoes phase separation. Individually removing the H3 and H4 tails abrogates phase separation under the same conditions. Taking a reductionist approach to investigate H3 and H4 tail peptide interactions in-trans with DNA and nucleosome core particles supports the direct involvement of these tails in chromatin phase separation. These results provide insight into fundamental mechanisms underlying phase separation of chromatin, which starts at the level of the nucleosome core particle, and support that long-range inter-nucleosomal interactions are sufficient to drive phase separation at nuclear concentrations. Additionally, our data have implications for understanding crosstalk between histone tails and provide a lens through which to interpret the effect of histone post-translational modifications and sequence variants. STATEMENT OF SIGNIFICANCE: Emerging models propose that chromatin organization is based in phase separation, however, mechanisms that drive this dynamic nuclear organization are only beginning to be understood. Previous focus has been on phase separation driven by chromatin-associating proteins, but this has recently shifted to recognize a direct role of chromatin in phase separation. Here, we take a fundamental approach in understanding chromatin phase separation and present new findings that the basic subunit of chromatin, the nucleosome core particle, undergoes phase separation under physiological concentrations of nucleosome and monovalent salt. Furthermore, the histone H3 and H4 tails are involved in phase separation in a manner independent of histone-associating proteins. These data suggest that H3 and H4 tail epigenetic factors may modulate chromatin phase separation.
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Affiliation(s)
- Erin F Hammonds
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - Megan Cleland Harwig
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - Emeleeta A Paintsil
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - Emma A Tillison
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America; Medical Scientist Training Program, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America
| | - Emma A Morrison
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, United States of America.
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13
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Swygert SG, Lin D, Portillo-Ledesma S, Lin PY, Hunt DR, Kao CF, Schlick T, Noble WS, Tsukiyama T. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. eLife 2021; 10:e72062. [PMID: 34734806 PMCID: PMC8598167 DOI: 10.7554/elife.72062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
A longstanding hypothesis is that chromatin fiber folding mediated by interactions between nearby nucleosomes represses transcription. However, it has been difficult to determine the relationship between local chromatin fiber compaction and transcription in cells. Further, global changes in fiber diameters have not been observed, even between interphase and mitotic chromosomes. We show that an increase in the range of local inter-nucleosomal contacts in quiescent yeast drives the compaction of chromatin fibers genome-wide. Unlike actively dividing cells, inter-nucleosomal interactions in quiescent cells require a basic patch in the histone H4 tail. This quiescence-specific fiber folding globally represses transcription and inhibits chromatin loop extrusion by condensin. These results reveal that global changes in chromatin fiber compaction can occur during cell state transitions, and establish physiological roles for local chromatin fiber folding in regulating transcription and chromatin domain formation.
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Affiliation(s)
- Sarah G Swygert
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Dejun Lin
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | | | - Po-Yen Lin
- Institute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Dakota R Hunt
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Tamar Schlick
- Department of Chemistry, New York UniversityNew YorkUnited States
- Courant Institute of Mathematical Sciences, New York UniversityNew YorkUnited States
- New York University-East China Normal University Center for Computational Chemistry at New York University ShanghaiShanghaiChina
| | - William S Noble
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Paul G. Allen School of Computer Science and Engineering, University of WashingtonSeattleUnited States
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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14
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Hansen JC, Maeshima K, Hendzel MJ. The solid and liquid states of chromatin. Epigenetics Chromatin 2021; 14:50. [PMID: 34717733 PMCID: PMC8557566 DOI: 10.1186/s13072-021-00424-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
The review begins with a concise description of the principles of phase separation. This is followed by a comprehensive section on phase separation of chromatin, in which we recount the 60 years history of chromatin aggregation studies, discuss the evidence that chromatin aggregation intrinsically is a physiologically relevant liquid-solid phase separation (LSPS) process driven by chromatin self-interaction, and highlight the recent findings that under specific solution conditions chromatin can undergo liquid-liquid phase separation (LLPS) rather than LSPS. In the next section of the review, we discuss how certain chromatin-associated proteins undergo LLPS in vitro and in vivo. Some chromatin-binding proteins undergo LLPS in purified form in near-physiological ionic strength buffers while others will do so only in the presence of DNA, nucleosomes, or chromatin. The final section of the review evaluates the solid and liquid states of chromatin in the nucleus. While chromatin behaves as an immobile solid on the mesoscale, nucleosomes are mobile on the nanoscale. We discuss how this dual nature of chromatin, which fits well the concept of viscoelasticity, contributes to genome structure, emphasizing the dominant role of chromatin self-interaction.
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Affiliation(s)
- Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540, Japan.
| | - Michael J Hendzel
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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15
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Hananya N, Daley SK, Bagert JD, Muir TW. Synthesis of ADP-Ribosylated Histones Reveals Site-Specific Impacts on Chromatin Structure and Function. J Am Chem Soc 2021; 143:10847-10852. [PMID: 34264659 DOI: 10.1021/jacs.1c05429] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
ADP-ribosylation of nuclear proteins is a critical feature of various DNA damage repair pathways. Histones, particularly H3 and H2B, are major targets of ADP-ribosylation and are primarily modified on serine with a single ADP-ribose unit following DNA damage. While the overall impact of PARP1-dependent poly-ADP-ribosylation is heavily investigated, very little is known about the specific roles of histone ADP-ribosylation. Here, we report the development of an efficient and modular semisynthetic route to full-length ADP-ribosylated histones H3 and H2B, chemically installed at specific serine residues. The modified histones were used to generate various chemically defined ADP-ribosylated chromatin substrates, which were employed in biophysical assays. These studies revealed that ADP-ribosylation of serine-6 of histone H2B (H2BS6ADPr) inhibits chromatin folding and higher-order organization; notably, this effect was enhanced by ADP-ribosylation of H3S10. In addition, ADP-ribosylated nucleosomes were utilized in biochemical experiments employing a panel of lysine methyltransferase enzymes, revealing a context-dependent inhibition of histone H3K9 methylation. The availability of designer ADP-ribosylated chromatin described here is expected to facilitate further biochemical and structural studies regarding the roles of histone ADP-ribosylation in the DNA damage response.
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Affiliation(s)
- Nir Hananya
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sara K Daley
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - John D Bagert
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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16
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Höllmüller E, Geigges S, Niedermeier ML, Kammer KM, Kienle SM, Rösner D, Scheffner M, Marx A, Stengel F. Site-specific ubiquitylation acts as a regulator of linker histone H1. Nat Commun 2021; 12:3497. [PMID: 34108453 PMCID: PMC8190259 DOI: 10.1038/s41467-021-23636-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 05/03/2021] [Indexed: 01/05/2023] Open
Abstract
Decoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. This is well studied for PTMs of core histones but not for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the chemical synthesis of site-specifically mono-ubiquitylated H1.2 and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that site-specific ubiquitylation of H1 at position K64 modulates interactions with deubiquitylating enzymes and the deacetylase SIRT1. Moreover, it affects H1-dependent chromatosome assembly and phase separation resulting in a more open chromatosome conformation generally associated with a transcriptionally active chromatin state. In summary, we propose that site-specific ubiquitylation plays a general regulatory role for linker histone H1. While the role of specific posttranslational modifications (PTMs) is increasingly well understood for core histones, this is not the case for linker histone H1. Here the authors show that site-specific ubiquitylation of H1 results in distinct interactomes, regulates phase separation, and modulates assembly of chromatosomes.
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Affiliation(s)
- Eva Höllmüller
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Simon Geigges
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Marie L Niedermeier
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Kai-Michael Kammer
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Simon M Kienle
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Daniel Rösner
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Martin Scheffner
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Florian Stengel
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
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17
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Deckard CE, Sczepanski JT. Reversible chromatin condensation by the DNA repair and demethylation factor thymine DNA glycosylase. Nucleic Acids Res 2021; 49:2450-2459. [PMID: 33733652 PMCID: PMC7969020 DOI: 10.1093/nar/gkab040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 11/23/2022] Open
Abstract
Chromatin structures (and modulators thereof) play a central role in genome organization and function. Herein, we report that thymine DNA glycosylase (TDG), an essential enzyme involved in DNA repair and demethylation, has the capacity to alter chromatin structure directly through its physical interactions with DNA. Using chemically defined nucleosome arrays, we demonstrate that TDG induces decompaction of individual chromatin fibers upon binding and promotes self-association of nucleosome arrays into higher-order oligomeric structures (i.e. condensation). Chromatin condensation is mediated by TDG’s disordered polycationic N-terminal domain, whereas its C-terminal domain antagonizes this process. Furthermore, we demonstrate that TDG-mediated chromatin condensation is reversible by growth arrest and DNA damage 45 alpha (GADD45a), implying that TDG cooperates with its binding partners to dynamically control chromatin architecture. Finally, we show that chromatin condensation by TDG is sensitive to the methylation status of the underlying DNA. This new paradigm for TDG has specific implications for associated processes, such as DNA repair, DNA demethylation, and transcription, and general implications for the role of DNA modification ‘readers’ in controlling chromatin organization.
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Affiliation(s)
- Charles E Deckard
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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18
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Bowerman S, Wereszczynski J, Luger K. Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways. eLife 2021; 10:65587. [PMID: 33650488 PMCID: PMC7990501 DOI: 10.7554/elife.65587] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Eukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form ‘nucleosome-like’ complexes that continuously wind between 60 and 500 base pairs of DNA (‘archaeasomes’), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. Simulations reveal dynamics of increased accessibility without disruption of DNA-binding or tetramerization interfaces. Mg2+ concentration influences compaction, and cryoEM densities illustrate that DNA is wrapped in consecutive substates arranged 90o out-of-plane with one another. Without ATP-dependent remodelers, archaea may leverage these inherent dynamics to balance chromatin packing and accessibility. All animals, plants and fungi belong to a group of living organisms called eukaryotes. The two other groups are bacteria and archaea, which include unicellular, microscopic organisms. All three groups have genes, which are typically stored on long strands of DNA. Eukaryotes have so much DNA that they use proteins called histones to help package and organize it inside each cell. Archaea also have simplified histones that help store their DNA, and studying these proteins could reveal how eukaryotic histones first evolved. In eukaryotes, groups of eight histones form a short cylinder that organizes a small section of DNA into a structure called a nucleosome. Each cell needs hundreds of thousands of nucleosomes to arrange its DNA. Eukaryotic cells also contain other proteins that release pieces of DNA from histones so that their genetic information can be used. The histones in Archaea don’t form discrete nucleosomes, instead, they coil DNA into ‘slinky-like’ shapes. It’s still unclear how DNA packing in archaea works and how it differs from eukaryotes. Bowerman, Wereszczynski and Luger used computer simulations, biochemistry and cryo-electron microscopy to study the histones from archaea. The archaeal ‘slinky-like’ histone structures are more flexible than nucleosomes, and can open and close like clamshells. This flexibility allows the information in the genomes of Archaea to be easily accessed, so, unlike in eukaryotes, archaeal cells may not need other proteins to release the DNA from the histones. The ability to package DNA allows cells to contain many more genes, so evolving histones was a vital step in the evolution of eukaryotic life, including the appearance of animals. Archaeal histones may reflect early versions of histones in eukaryotes, and can be used to understand how DNA packing has evolved. Furthermore, a greater understanding of Archaea may help better explain their role in health and global ecosystems, and allow their use in industrial applications.
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Affiliation(s)
- Samuel Bowerman
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for the Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, United States
| | - Karolin Luger
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
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19
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Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome. Sci Rep 2021; 11:380. [PMID: 33432055 PMCID: PMC7801413 DOI: 10.1038/s41598-020-79654-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023] Open
Abstract
Linker histones play essential roles in the regulation and maintenance of the dynamic chromatin structure of higher eukaryotes. The influence of human histone H1.0 on the nucleosome structure and biophysical properties of the resulting chromatosome were investigated and compared with the 177-bp nucleosome using Cryo-EM and SAXS. The 4.5 Å Cryo-EM chromatosome structure showed that the linker histone binds at the nucleosome dyad interacting with both linker DNA arms but in a tilted manner leaning towards one of the linker sides. The chromatosome is laterally compacted and rigid in the dyad and linker DNA area, in comparison with the nucleosome where linker DNA region is more flexible and displays structural variability. In solution, the chromatosomes appear slightly larger than the nucleosomes, with the volume increase compared to the bound linker histone, according to solution SAXS measurements. SAXS X-ray diffraction characterisation of Mg-precipitated samples showed that the different shapes of the 177 chromatosome enabled the formation of a highly ordered lamello-columnar phase when precipitated by Mg2+, indicating the influence of linker histone on the nucleosome stacking. The biological significance of linker histone, therefore, may be affected by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in comparison to nucleosomes.
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20
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le Paige UB, Xiang S, Hendrix MMRM, Zhang Y, Folkers GE, Weingarth M, Bonvin AMJJ, Kutateladze TG, Voets IK, Baldus M, van Ingen H. Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:187-202. [PMID: 35647606 PMCID: PMC9135053 DOI: 10.5194/mr-2-187-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Regulation of DNA-templated processes such as gene transcription and DNA repair depend on the interaction of a wide range of proteins with the nucleosome, the fundamental building block of chromatin. Both solution and solid-state NMR spectroscopy have become an attractive approach to study the dynamics and interactions of nucleosomes, despite their high molecular weight of ~ 200 kDa. For solid-state NMR (ssNMR) studies, dilute solutions of nucleosomes are converted to a dense phase by sedimentation or precipitation. Since nucleosomes are known to self-associate, these dense phases may induce extensive interactions between nucleosomes, which could interfere with protein-binding studies. Here, we characterized the packing of nucleosomes in the dense phase created by sedimentation using NMR and small-angle X-ray scattering (SAXS) experiments. We found that nucleosome sediments are gels with variable degrees of solidity, have nucleosome concentration close to that found in crystals, and are stable for weeks under high-speed magic angle spinning (MAS). Furthermore, SAXS data recorded on recovered sediments indicate that there is no pronounced long-range ordering of nucleosomes in the sediment. Finally, we show that the sedimentation approach can also be used to study low-affinity protein interactions with the nucleosome. Together, our results give new insights into the sample characteristics of nucleosome sediments for ssNMR studies and illustrate the broad applicability of sedimentation-based NMR studies.
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Affiliation(s)
- Ulric B. le Paige
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - ShengQi Xiang
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Marco M. R. M. Hendrix
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gert E. Folkers
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Markus Weingarth
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Alexandre M. J. J. Bonvin
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ilja K. Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Marc Baldus
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Hugo van Ingen
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
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21
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Strickfaden H, Tolsma TO, Sharma A, Underhill DA, Hansen JC, Hendzel MJ. Condensed Chromatin Behaves like a Solid on the Mesoscale In Vitro and in Living Cells. Cell 2020; 183:1772-1784.e13. [PMID: 33326747 DOI: 10.1016/j.cell.2020.11.027] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/16/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022]
Abstract
The association of nuclear DNA with histones to form chromatin is essential for temporal and spatial control of eukaryotic genomes. In this study, we examined the physical state of condensed chromatin in vitro and in vivo. Our in vitro studies demonstrate that self-association of nucleosomal arrays under a wide range of solution conditions produces supramolecular condensates in which the chromatin is physically constrained and solid-like. By measuring DNA mobility in living cells, we show that condensed chromatin also exhibits solid-like behavior in vivo. Representative heterochromatin proteins, however, display liquid-like behavior and coalesce around the solid chromatin scaffold. Importantly, euchromatin and heterochromatin show solid-like behavior even under conditions that produce limited interactions between chromatin fibers. Our results reveal that condensed chromatin exists in a solid-like state whose properties resist external forces and create an elastic gel and provides a scaffold that supports liquid-liquid phase separation of chromatin binding proteins.
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Affiliation(s)
- Hilmar Strickfaden
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Thomas O Tolsma
- Department of Biochemistry and Molecular Biology, College of Natural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ajit Sharma
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - D Alan Underhill
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, College of Natural Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Michael J Hendzel
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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22
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Beads on a string-nucleosome array arrangements and folding of the chromatin fiber. Nat Struct Mol Biol 2020; 27:109-118. [PMID: 32042149 DOI: 10.1038/s41594-019-0368-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022]
Abstract
Understanding how the genome is structurally organized as chromatin is essential for understanding its function. Here, we review recent developments that allowed the readdressing of old questions regarding the primary level of chromatin structure, the arrangement of nucleosomes along the DNA and the folding of the nucleosome fiber in nuclear space. In contrast to earlier views of nucleosome arrays as uniformly regular and folded, recent findings reveal heterogeneous array organization and diverse modes of folding. Local structure variations reflect a continuum of functional states characterized by differences in post-translational histone modifications, associated chromatin-interacting proteins and nucleosome-remodeling enzymes.
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23
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Grigoryev SA, Popova EY. Attraction of Likenesses: Mechanisms of Self-Association and Compartmentalization of Eukaryotic Chromatin. Mol Biol 2019. [DOI: 10.1134/s0026893319060050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Dacher M, Tachiwana H, Horikoshi N, Kujirai T, Taguchi H, Kimura H, Kurumizaka H. Incorporation and influence of Leishmania histone H3 in chromatin. Nucleic Acids Res 2019; 47:11637-11648. [PMID: 31722422 PMCID: PMC7145708 DOI: 10.1093/nar/gkz1040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Immunopathologies caused by Leishmania cause severe human morbidity and mortality. This protozoan parasite invades and persists inside host cells, resulting in disease development. Leishmania modifies the epigenomic status of the host cells, thus probably averting the host cell defense mechanism. To accomplish this, Leishmania may change the host cell chromatin structure. However, the mechanism by which the parasite changes the host cell chromatin has not been characterized. In the present study, we found that ectopically produced Leishmania histone H3, LmaH3, which mimics the secreted LmaH3 in infected cells, is incorporated into chromatin in human cells. A crystallographic analysis revealed that LmaH3 forms nucleosomes with human histones H2A, H2B and H4. We found that LmaH3 was less stably incorporated into the nucleosome, as compared to human H3.1. Consistently, we observed that LmaH3-H4 association was remarkably weakened. Mutational analyses revealed that the specific LmaH3 Trp35, Gln57 and Met98 residues, which correspond to the H3.1 Tyr41, Arg63 and Phe104 residues, might be responsible for the instability of the LmaH3 nucleosome. Nucleosomes containing LmaH3 resisted the Mg2+-mediated compaction of the chromatin fiber. These distinct physical characteristics of LmaH3 support the possibility that histones secreted by parasites during infection may modulate the host chromatin structure.
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Affiliation(s)
- Mariko Dacher
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroaki Tachiwana
- Department of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Naoki Horikoshi
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroyuki Taguchi
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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25
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Ohyama T. New Aspects of Magnesium Function: A Key Regulator in Nucleosome Self-Assembly, Chromatin Folding and Phase Separation. Int J Mol Sci 2019; 20:ijms20174232. [PMID: 31470631 PMCID: PMC6747271 DOI: 10.3390/ijms20174232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 02/07/2023] Open
Abstract
Metal cations are associated with many biological processes. The effects of these cations on nucleic acids and chromatin were extensively studied in the early stages of nucleic acid and chromatin research. The results revealed that some monovalent and divalent metal cations, including Mg2+, profoundly affect the conformations and stabilities of nucleic acids, the folding of chromatin fibers, and the extent of chromosome condensation. Apart from these effects, there have only been a few reports on the functions of these cations. In 2007 and 2013, however, Mg2+-implicated novel phenomena were found: Mg2+ facilitates or enables both self-assembly of identical double-stranded (ds) DNA molecules and self-assembly of identical nucleosomes in vitro. These phenomena may be deeply implicated in the heterochromatin domain formation and chromatin-based phase separation. Furthermore, a recent study showed that elevation of the intranuclear Mg2+ concentration causes unusual differentiation of mouse ES (embryonic stem) cells. All of these phenomena seem to be closely related to one another. Mg2+ seems to be a key regulator of chromatin dynamics and chromatin-based biological processes.
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Affiliation(s)
- Takashi Ohyama
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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26
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Post-translational modifications and chromatin dynamics. Essays Biochem 2019; 63:89-96. [DOI: 10.1042/ebc20180067] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/21/2022]
Abstract
Abstract
The dynamic structure of chromatin is linked to gene regulation and many other biological functions. Consequently, it is of importance to understand the factors that regulate chromatin dynamics. While the in vivo analysis of chromatin has verified that histone post-translational modifications play a role in modulating DNA accessibility, the complex nuclear environment and multiplicity of modifications prevents clear conclusions as to how individual modifications influence chromatin dynamics in the cell. For this reason, in vitro analyses of model reconstituted nucleosomal arrays has been pivotal in understanding the dynamic nature of chromatin compaction and the affects that specific post-translational modifications can have on the higher order chromatin structure. In this mini-review, we briefly describe the dynamic chromatin structures that have been observed in vitro and the environmental conditions that give rise to these various conformational states. Our focus then turns to a discussion of the specific histone post-translational modifications that have been shown to alter formation of these higher order chromatin structures in vitro and how this may relate to the biological state and accessibility of chromatin in vivo.
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27
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Osunsade A, Prescott NA, Hebert JM, Ray DM, Jmeian Y, Lorenz IC, David Y. A Robust Method for the Purification and Characterization of Recombinant Human Histone H1 Variants. Biochemistry 2019; 58:171-176. [PMID: 30585724 PMCID: PMC6541009 DOI: 10.1021/acs.biochem.8b01060] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Higher order compaction of the eukaryotic genome is key to the regulation of all DNA-templated processes, including transcription. This tightly controlled process involves the formation of mononucleosomes, the fundamental unit of chromatin, packaged into higher order architectures in an H1 linker histone-dependent process. While much work has been done to delineate the precise mechanism of this event in vitro and in vivo, major gaps still exist, primarily due to a lack of molecular tools. Specifically, there has never been a successful purification and biochemical characterization of all human H1 variants. Here we present a robust method to purify H1 and illustrate its utility in the purification of all somatic variants and one germline variant. In addition, we performed a first ever side-by-side biochemical comparison, which revealed a gradient of nucleosome binding affinities and compaction capabilities. These data provide new insight into H1 redundancy and lay the groundwork for the mechanistic investigation of disease-driving mutations.
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Affiliation(s)
- Adewola Osunsade
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
| | - Jakob M. Hebert
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
| | - Devin M. Ray
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
- Tri-Institutional MD-PhD Program, New York, NY
| | - Yazen Jmeian
- Tri-Institutional Therapeutics Discovery Institute, New York, NY
| | - Ivo C. Lorenz
- Tri-Institutional Therapeutics Discovery Institute, New York, NY
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional PhD Program in Chemical Biology, New York, NY
- Department of Pharmacology, Weill Cornell Medical College, New York, NY
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY
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28
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Bass MV, Nikitina T, Norouzi D, Zhurkin VB, Grigoryev SA. Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays. J Biol Chem 2019; 294:4233-4246. [PMID: 30630950 DOI: 10.1074/jbc.ra118.006412] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/04/2019] [Indexed: 01/09/2023] Open
Abstract
The length of linker DNA that separates nucleosomes is highly variable, but its mechanistic role in modulating chromatin structure and functions remains unknown. Here, we established an experimental system using circular arrays of positioned nucleosomes to investigate whether variations in nucleosome linker length could affect nucleosome folding, self-association, and interactions. We conducted EM, DNA topology, native electrophoretic assays, and Mg2+-dependent self-association assays to study intrinsic folding of linear and circular nucleosome arrays with linker DNA length of 36 bp and 41 bp (3.5 turns and 4 turns of DNA double helix, respectively). These experiments revealed that potential artifacts arising from open DNA ends and full DNA relaxation in the linear arrays do not significantly affect overall chromatin compaction and self-association. We observed that the 0.5 DNA helical turn difference between the two DNA linker lengths significantly affects DNA topology and nucleosome interactions. In particular, the 41-bp linkers promoted interactions between any two nucleosome beads separated by one bead as expected for a zigzag fiber, whereas the 36-bp linkers promoted interactions between two nucleosome beads separated by two other beads and also reduced negative superhelicity. Monte Carlo simulations accurately reproduce periodic modulations of chromatin compaction, DNA topology, and internucleosomal interactions with a 10-bp periodicity. We propose that the nucleosome spacing and associated chromatin structure modulations may play an important role in formation of different chromatin epigenetic states, thus suggesting implications for how chromatin accessibility to DNA-binding factors and the RNA transcription machinery is regulated.
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Affiliation(s)
- Mikhail V Bass
- From the Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033.,Biological Faculty, Department of Molecular Biology, Lomonosov Moscow State University, 119192 Moscow, Russia, and
| | - Tatiana Nikitina
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Davood Norouzi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Victor B Zhurkin
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Sergei A Grigoryev
- From the Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033,
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29
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Mishra LN, Hayes JJ. A nucleosome-free region locally abrogates histone H1-dependent restriction of linker DNA accessibility in chromatin. J Biol Chem 2018; 293:19191-19200. [PMID: 30373774 DOI: 10.1074/jbc.ra118.005721] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/16/2018] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic genomes are packaged into linker-oligonucleosome assemblies, providing compaction of genomic DNA and contributing to gene regulation and genome integrity. To define minimal requirements for initial steps in the transition of compact, closed chromatin to a transcriptionally active, open state, we developed a model in vitro system containing a single, unique, "target" nucleosome in the center of a 25-nucleosome array and evaluated the accessibility of the linker DNA adjacent to this target nucleosome. We found that condensation of H1-lacking chromatin results in ∼60-fold reduction in linker DNA accessibility and that mimics of acetylation within all four core histone tail domains of the target nucleosome synergize to increase accessibility ∼3-fold. Notably, stoichiometric binding of histone H1 caused >2 orders of magnitude reduction in accessibility that was marginally diminished by histone acetylation mimics. Remarkably, a nucleosome-free region (NFR) in place of the target nucleosome completely abrogated H1-dependent restriction of linker accessibility in the immediate vicinity of the NFR. Our results suggest that linker DNA is as inaccessible as DNA within the nucleosome core in fully condensed, H1-containing chromatin. They further imply that an unrecognized function of NFRs in gene promoter regions is to locally abrogate the severe restriction of linker DNA accessibility imposed by H1s.
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Affiliation(s)
- Laxmi Narayan Mishra
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
| | - Jeffrey J Hayes
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
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30
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Zinchenko A, Berezhnoy NV, Chen Q, Nordenskiöld L. Compaction of Single-Molecule Megabase-Long Chromatin under the Influence of Macromolecular Crowding. Biophys J 2018; 114:2326-2335. [PMID: 29729833 PMCID: PMC6129467 DOI: 10.1016/j.bpj.2018.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/05/2018] [Accepted: 04/02/2018] [Indexed: 12/21/2022] Open
Abstract
The megabase-sized length of chromatin is highly relevant to the state of chromatin in vivo, where it is subject to a highly crowded environment and is organized in topologically associating domains of similar dimension. We developed an in vitro experimental chromatin model system reconstituted from T4 DNA (approximately 166 kbp) and histone octamers and studied the monomolecular compaction of this megabase-sized chromatin fiber under the influence of macromolecular crowding. We used single-molecule fluorescence microscopy and observed compaction in aqueous solutions containing poly(ethylene glycol) in the presence of monovalent (Na+ and K+) and divalent (Mg2+) cations. Both DNA and chromatin demonstrated compaction under comparable conditions in the presence of poly(ethylene glycol) and Na+ or Mg2+ salt. However, the mechanism of the compaction changed from a first-order phase transition for DNA to a continuous folding for megabase-sized chromatin fibers. A more efficient and pronounced chromatin compaction was observed in the presence of Na+ compared to K+. A flow-stretching technique to unfold DNA and chromatin coils was used to gain further insight into the morphology of partially folded chromatin fibers. The results revealed a distribution of partially folded chromatin fibers. This variability is likely the result of the heterogeneous distribution of nucleosomes on the DNA chain. The packaging of DNA in the form of chromatin in the crowded nuclear environment appears essential to ensure gradual conformational changes of DNA.
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Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Qinming Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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31
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Limouse C, Bell JC, Fuller CJ, Straight AF, Mabuchi H. Measurement of Mesoscale Conformational Dynamics of Freely Diffusing Molecules with Tracking FCS. Biophys J 2018; 114:1539-1550. [PMID: 29642025 PMCID: PMC5954409 DOI: 10.1016/j.bpj.2018.01.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/27/2017] [Accepted: 01/02/2018] [Indexed: 11/19/2022] Open
Abstract
Few techniques are suited to probe the structure and dynamics of molecular complexes at the mesoscale level (∼100-1000 nm). We have developed a single-molecule technique that uses tracking fluorescence correlation spectroscopy (tFCS) to probe the conformation and dynamics of mesoscale molecular assemblies. tFCS measures the distance fluctuations between two fluorescently labeled sites within an untethered, freely diffusing biomolecule. To achieve subdiffraction spatial resolution, we developed a feedback scheme that allows us to maintain the molecule at an optimal position within the laser intensity gradient for fluorescence correlation spectroscopy. We characterized tFCS spatial sensitivity by measuring the Brownian end-to-end dynamics of DNA molecules as short as 1000 bp. We demonstrate that tFCS detects changes in the compaction of reconstituted nucleosome arrays and can assay transient protein-mediated interactions between distant sites in an individual DNA molecule. Our measurements highlight the applicability of tFCS to a wide variety of biochemical processes involving mesoscale conformational dynamics.
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Affiliation(s)
| | - Jason C Bell
- Department of Biochemistry, Stanford University, Stanford, California
| | - Colin J Fuller
- Department of Biochemistry, Stanford University, Stanford, California
| | - Aaron F Straight
- Department of Biochemistry, Stanford University, Stanford, California.
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32
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Zinchenko A, Berezhnoy NV, Wang S, Rosencrans WM, Korolev N, van der Maarel JR, Nordenskiöld L. Single-molecule compaction of megabase-long chromatin molecules by multivalent cations. Nucleic Acids Res 2018; 46:635-649. [PMID: 29145649 PMCID: PMC5778610 DOI: 10.1093/nar/gkx1135] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 10/18/2017] [Accepted: 10/29/2017] [Indexed: 11/21/2022] Open
Abstract
To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo. Variation of HO loading revealed a number of unique features related to the efficiency of chromatin compaction by multivalent cations, the mechanism of compaction, and the character of partly compact chromatin structures. The observations may be relevant for how DNA accessibility in chromatin is maintained. Compaction of saturated chromatin, in turn, is accompanied by an intra-chain segregation at the level of single chromatin molecules, suggesting an intriguing scenario of selective activation/deactivation of DNA as a result of chromatin fiber heterogeneity due to the nucleosome positioning. We suggest that this chromatin, reconstituted on megabase-long DNA because of its large size, is a useful model of eukaryotic chromatin.
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Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Sai Wang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - William M Rosencrans
- Department of Physics and Astronomy, Colgate University, Hamilton, NY 13346, USA
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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33
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The 10-nm chromatin fiber and its relationship to interphase chromosome organization. Biochem Soc Trans 2017; 46:67-76. [PMID: 29263138 PMCID: PMC5818668 DOI: 10.1042/bst20170101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/09/2023]
Abstract
A chromosome is a single long DNA molecule assembled along its length with nucleosomes and proteins. During interphase, a mammalian chromosome exists as a highly organized supramolecular globule in the nucleus. Here, we discuss new insights into how genomic DNA is packaged and organized within interphase chromosomes. Our emphasis is on the structural principles that underlie chromosome organization, with a particular focus on the intrinsic contributions of the 10-nm chromatin fiber, but not the regular 30-nm fiber. We hypothesize that the hierarchical globular organization of an interphase chromosome is fundamentally established by the self-interacting properties of a 10-nm zig-zag array of nucleosomes, while histone post-translational modifications, histone variants, and chromatin-associated proteins serve to mold generic chromatin domains into specific structural and functional entities.
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34
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Buckwalter JM, Norouzi D, Harutyunyan A, Zhurkin VB, Grigoryev SA. Regulation of chromatin folding by conformational variations of nucleosome linker DNA. Nucleic Acids Res 2017; 45:9372-9387. [PMID: 28934465 PMCID: PMC5766201 DOI: 10.1093/nar/gkx562] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/19/2017] [Indexed: 11/16/2022] Open
Abstract
Linker DNA conformational variability has been proposed to direct nucleosome array folding into more or less compact chromatin fibers but direct experimental evidence for such models are lacking. Here, we tested this hypothesis by designing nucleosome arrays with A-tracts at specific locations in the nucleosome linkers to induce inward (AT-IN) and outward (AT-OUT) bending of the linker DNA. Using electron microscopy and analytical centrifugation techniques, we observed spontaneous folding of AT-IN nucleosome arrays into highly compact structures, comparable to those induced by linker histone H1. In contrast, AT-OUT nucleosome arrays formed less compact structures with decreased nucleosome interactions similar to wild-type nucleosome arrays. Adding linker histone H1 further increased compaction of the A-tract arrays while maintaining structural differences between them. Furthermore, restriction nuclease digestion revealed a strongly reduced accessibility of nucleosome linkers in the compact AT-IN arrays. Electron microscopy analysis and 3D computational Monte Carlo simulations are consistent with a profound zigzag linker DNA configuration and closer nucleosome proximity in the AT-IN arrays due to inward linker DNA bending. We propose that the evolutionary preferred positioning of A-tracts in DNA linkers may control chromatin higher-order folding and thus influence cellular processes such as gene expression, transcription and DNA repair.
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Affiliation(s)
- Jenna M Buckwalter
- Penn State University College of Medicine, Department of Biochemistry and Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA
| | - Davood Norouzi
- Laboratory of Cell Biology, CCR, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anna Harutyunyan
- Penn State University College of Medicine, Department of Biochemistry and Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, CCR, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sergei A Grigoryev
- Penn State University College of Medicine, Department of Biochemistry and Molecular Biology, H171, Milton S. Hershey Medical Center, P.O. Box 850, 500 University Drive, Hershey, PA 17033, USA
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35
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Murphy KJ, Cutter AR, Fang H, Postnikov YV, Bustin M, Hayes JJ. HMGN1 and 2 remodel core and linker histone tail domains within chromatin. Nucleic Acids Res 2017; 45:9917-9930. [PMID: 28973435 PMCID: PMC5622319 DOI: 10.1093/nar/gkx579] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/28/2017] [Indexed: 01/23/2023] Open
Abstract
The structure of the nucleosome, the basic building block of the chromatin fiber, plays a key role in epigenetic regulatory processes that affect DNA-dependent processes in the context of chromatin. Members of the HMGN family of proteins bind specifically to nucleosomes and affect chromatin structure and function, including transcription and DNA repair. To better understand the mechanisms by which HMGN 1 and 2 alter chromatin, we analyzed their effect on the organization of histone tails and linker histone H1 in nucleosomes. We find that HMGNs counteract linker histone (H1)-dependent stabilization of higher order ‘tertiary’ chromatin structures but do not alter the intrinsic ability of nucleosome arrays to undergo salt-induced compaction and self-association. Surprisingly, HMGNs do not displace H1s from nucleosomes; rather these proteins bind nucleosomes simultaneously with H1s without disturbing specific contacts between the H1 globular domain and nucleosomal DNA. However, HMGNs do alter the nucleosome-dependent condensation of the linker histone C-terminal domain, which is critical for stabilizing higher-order chromatin structures. Moreover, HMGNs affect the interactions of the core histone tail domains with nucleosomal DNA, redirecting the tails to more interior positions within the nucleosome. Our studies provide new insights into the molecular mechanisms whereby HMGNs affect chromatin structure.
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Affiliation(s)
- Kevin J Murphy
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - Amber R Cutter
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - He Fang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - Yuri V Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
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36
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Zhiteneva A, Bonfiglio JJ, Makarov A, Colby T, Vagnarelli P, Schirmer EC, Matic I, Earnshaw WC. Mitotic post-translational modifications of histones promote chromatin compaction in vitro. Open Biol 2017; 7:170076. [PMID: 28903997 PMCID: PMC5627050 DOI: 10.1098/rsob.170076] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/27/2017] [Indexed: 02/01/2023] Open
Abstract
How eukaryotic chromosomes are compacted during mitosis has been a leading question in cell biology since the nineteenth century. Non-histone proteins such as condensin complexes contribute to chromosome shaping, but appear not to be necessary for mitotic chromatin compaction. Histone modifications are known to affect chromatin structure. As histones undergo major changes in their post-translational modifications during mitotic entry, we speculated that the spectrum of cell-cycle-specific histone modifications might contribute to chromosome compaction during mitosis. To test this hypothesis, we isolated core histones from interphase and mitotic cells and reconstituted chromatin with them. We used mass spectrometry to show that key post-translational modifications remained intact during our isolation procedure. Light, atomic force and transmission electron microscopy analysis showed that chromatin assembled from mitotic histones has a much greater tendency to aggregate than chromatin assembled from interphase histones, even under low magnesium conditions where interphase chromatin remains as separate beads-on-a-string structures. These observations are consistent with the hypothesis that mitotic chromosome formation is a two-stage process with changes in the spectrum of histone post-translational modifications driving mitotic chromatin compaction, while the action of non-histone proteins such as condensin may then shape the condensed chromosomes into their classic mitotic morphology.
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Affiliation(s)
- Alisa Zhiteneva
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Juan Jose Bonfiglio
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne 50931, Germany
| | - Alexandr Makarov
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Thomas Colby
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne 50931, Germany
| | - Paola Vagnarelli
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Institute of Environment, Health and Society, Department of Life Sciences, Brunel University London, Heinz Wolff Building, Uxbridge UB8 3PH, UK
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne 50931, Germany
| | - William C Earnshaw
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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37
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Murata A, Itoh Y, Mano E, Kanbayashi S, Igarashi C, Takahashi H, Takahashi S, Kamagata K. One-Dimensional Search Dynamics of Tumor Suppressor p53 Regulated by a Disordered C-Terminal Domain. Biophys J 2017; 112:2301-2314. [PMID: 28591603 DOI: 10.1016/j.bpj.2017.04.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 04/06/2017] [Accepted: 04/25/2017] [Indexed: 11/15/2022] Open
Abstract
Tumor suppressor p53 slides along DNA and finds its target sequence in drastically different and changing cellular conditions. To elucidate how p53 maintains efficient target search at different concentrations of divalent cations such as Ca2+ and Mg2+, we prepared two mutants of p53, each possessing one of its two DNA-binding domains, the CoreTet mutant having the structured core domain plus the tetramerization (Tet) domain, and the TetCT mutant having Tet plus the disordered C-terminal domain. We investigated their equilibrium and kinetic dissociation from DNA and search dynamics along DNA at various [Mg2+]. Although binding of CoreTet to DNA becomes markedly weaker at higher [Mg2+], binding of TetCT depends slightly on [Mg2+]. Single-molecule fluorescence measurements revealed that the one-dimensional diffusion of CoreTet along DNA consists of fast and slow search modes, the ratio of which depends strongly on [Mg2+]. In contrast, diffusion of TetCT consisted of only the fast mode. The disordered C-terminal domain can associate with DNA irrespective of [Mg2+], and can maintain an equilibrium balance of the two search modes and the p53 search distance. These results suggest that p53 modulates the quaternary structure of the complex between p53 and DNA under different [Mg2+] and that it maintains the target search along DNA.
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Affiliation(s)
- Agato Murata
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Saori Kanbayashi
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Chihiro Igarashi
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Hiroto Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan.
| | - Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan.
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38
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Nizovtseva EV, Todolli S, Olson WK, Studitsky VM. Towards quantitative analysis of gene regulation by enhancers. Epigenomics 2017; 9:1219-1231. [PMID: 28799793 DOI: 10.2217/epi-2017-0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enhancers are regulatory DNA sequences that can activate transcription over large distances. Recent studies have revealed the widespread role of distant activation in eukaryotic gene regulation and in the development of various human diseases, including cancer. Here we review recent progress in the field, focusing on new experimental and computational approaches that quantify the role of chromatin structure and dynamics during enhancer-promoter interactions in vitro and in vivo.
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Affiliation(s)
- Ekaterina V Nizovtseva
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA
| | - Stefjord Todolli
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Wilma K Olson
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854, USA
| | - Vasily M Studitsky
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Ave., Philadelphia, PA 19422, USA.,Biology Faculty, Moscow State University, Moscow 119991, Russia.,Laboratory of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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39
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Amamoto Y, Aoi Y, Nagashima N, Suto H, Yoshidome D, Arimura Y, Osakabe A, Kato D, Kurumizaka H, Kawashima SA, Yamatsugu K, Kanai M. Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin. J Am Chem Soc 2017; 139:7568-7576. [DOI: 10.1021/jacs.7b02138] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yoshifumi Amamoto
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST-ERATO, Kanai Life Science Catalysis Project, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuki Aoi
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST-ERATO, Kanai Life Science Catalysis Project, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Nozomu Nagashima
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroki Suto
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST-ERATO, Kanai Life Science Catalysis Project, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Daisuke Yoshidome
- Schrödinger K. K., 17F Marunouchi
Trust Tower North, 1-8-1 Marunouchi Chiyoda-ku, Tokyo 100-0005, 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
| | - 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
| | - Daiki Kato
- Laboratory
of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku,
Tokyo 162-8480, 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
| | - Shigehiro A. Kawashima
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST-ERATO, Kanai Life Science Catalysis Project, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kenzo Yamatsugu
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST-ERATO, Kanai Life Science Catalysis Project, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- JST-ERATO, Kanai Life Science Catalysis Project, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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40
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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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41
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Kujirai T, Machida S, Osakabe A, Kurumizaka H. Influence of polynucleosome preparation methods on sedimentation velocity analysis of chromatin. J Biochem 2016; 161:381-388. [DOI: 10.1093/jb/mvw081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/03/2016] [Indexed: 01/09/2023] Open
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42
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Todolli S, Perez PJ, Clauvelin N, Olson WK. Contributions of Sequence to the Higher-Order Structures of DNA. Biophys J 2016; 112:416-426. [PMID: 27955889 DOI: 10.1016/j.bpj.2016.11.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/11/2016] [Accepted: 11/15/2016] [Indexed: 11/17/2022] Open
Abstract
One of the critical unanswered questions in genome biophysics is how the primary sequence of DNA bases influences the global properties of very-long-chain molecules. The local sequence-dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate the global folding and interactions of double helices with hundreds of basepairs. These features also determine the positions of nucleosomes on DNA and the lengths of the interspersed DNA linkers. Like the patterns of basepair association within DNA, the arrangements of nucleosomes in chromatin modulate the properties of longer polymers. The intrachromosomal loops detected in genomic studies contain hundreds of nucleosomes, and given that the simulated configurations of chromatin depend on the lengths of linker DNA, the formation of these loops may reflect sequence-dependent information encoded within the positioning of the nucleosomes. With knowledge of the positions of nucleosomes on a given genome, methods are now at hand to estimate the looping propensities of chromatin in terms of the spacing of nucleosomes and to make a direct connection between the DNA base sequence and larger-scale chromatin folding.
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Affiliation(s)
- Stefjord Todolli
- Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Pamela J Perez
- Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Nicolas Clauvelin
- Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Wilma K Olson
- Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, New Jersey; Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey.
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43
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Ubiquitin utilizes an acidic surface patch to alter chromatin structure. Nat Chem Biol 2016; 13:105-110. [PMID: 27870837 PMCID: PMC5161692 DOI: 10.1038/nchembio.2235] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/07/2016] [Indexed: 02/06/2023]
Abstract
Ubiquitylation of histone H2B, associated with gene activation, leads to chromatin decompaction through an unknown mechanism. We used a hydrogen-deuterium exchange strategy coupled with nuclear magnetic resonance spectroscopy to map the ubiquitin surface responsible for its structural effects on chromatin. Our studies revealed that a previously uncharacterized acidic patch on ubiquitin comprising residues Glu16 and Glu18 is essential for decompaction. These residues mediate promiscuous electrostatic interactions with the basic histone proteins, potentially positioning the ubiquitin moiety as a dynamic “wedge” that prevents the intimate association of neighboring nucleosomes. Using two independent cross-linking strategies and an oligomerization assay, we also showed that ubiquitin-ubiquitin contacts occur in the chromatin environment and are important for the solubilization of the chromatin polymers. Our work highlights a novel, chromatin-related aspect of the “ubiquitin code”, and sheds light on how the information rich ubiquitin modification can orchestrate different biochemical outcomes using different surface features.
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44
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Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays. Sci Rep 2016; 6:34808. [PMID: 27708426 PMCID: PMC5052607 DOI: 10.1038/srep34808] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/20/2016] [Indexed: 12/21/2022] Open
Abstract
The activation of a silent gene locus is thought to involve pioneering transcription factors that initiate changes in the local chromatin structure to increase promoter accessibility and binding of downstream effectors. To better understand the molecular requirements for the first steps of locus activation, we investigated whether acetylation of a single nucleosome is sufficient to alter DNA accessibility within a condensed 25-nucleosome array. We found that acetylation mimics within the histone H4 tail domain increased accessibility of the surrounding linker DNA, with the increased accessibility localized to the immediate vicinity of the modified nucleosome. In contrast, acetylation mimics within the H3 tail had little effect, but were able to synergize with H4 tail acetylation mimics to further increase accessibility. Moreover, replacement of the central nucleosome with a nucleosome free region also resulted in increased local, but not global DNA accessibility. Our results indicate that modification or disruption of only a single target nucleosome results in significant changes in local chromatin architecture and suggest that very localized chromatin modifications imparted by pioneer transcription factors are sufficient to initiate a cascade of events leading to promoter activation.
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45
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Riedmann C, Fondufe-Mittendorf YN. Comparative analysis of linker histone H1, MeCP2, and HMGD1 on nucleosome stability and target site accessibility. Sci Rep 2016; 6:33186. [PMID: 27624769 PMCID: PMC5021983 DOI: 10.1038/srep33186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 08/23/2016] [Indexed: 12/15/2022] Open
Abstract
Chromatin architectural proteins (CAPs) bind the entry/exit DNA of nucleosomes and linker DNA to form higher order chromatin structures with distinct transcriptional outcomes. How CAPs mediate nucleosome dynamics is not well understood. We hypothesize that CAPs regulate DNA target site accessibility through alteration of the rate of spontaneous dissociation of DNA from nucleosomes. We investigated the effects of histone H1, high mobility group D1 (HMGD1), and methyl CpG binding protein 2 (MeCP2), on the biophysical properties of nucleosomes and chromatin. We show that MeCP2, like the repressive histone H1, traps the nucleosome in a more compact mononucleosome structure. Furthermore, histone H1 and MeCP2 hinder model transcription factor Gal4 from binding to its cognate DNA site within the nucleosomal DNA. These results demonstrate that MeCP2 behaves like a repressor even in the absence of methylation. Additionally, MeCP2 behaves similarly to histone H1 and HMGD1 in creating a higher-order chromatin structure, which is susceptible to chromatin remodeling by ISWI. Overall, we show that CAP binding results in unique changes to nucleosome structure and dynamics.
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Affiliation(s)
- Caitlyn Riedmann
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
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46
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Nurse NP, Yuan C. Cis and trans internucleosomal interactions of H3 and H4 tails in tetranucleosomes. Biopolymers 2016; 103:33-40. [PMID: 25196374 DOI: 10.1002/bip.22560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 08/22/2014] [Indexed: 11/09/2022]
Abstract
Chromatin structure and the transcriptional state of a gene can be modulated by modifications made on H3 and H4 tails of histones. Elucidating the internucleosomal interactions of these tails is vital to understanding epigenetic regulation. Differentiation between cis (intra-nucleosomal) and trans (inter-nucleosomal) interactions is often difficult with conventional techniques since H3 and H4 tails are flexible. The distinction, however, is important because these interactions model short- and long-range chromatin interactions respectively and have different bearings in biological processes. Combining FCS and PCH analysis, we can decouple the contribution of histone tails to cis and trans effects. A Mg(2+) gradient was employed to facilitate compaction and oligomerization of tetranucleosomes with H3 and/or H4 tail truncations. H3 tails were found to play a multifunctional role and exhibit the ability to partake in both attractive cis and trans interactions simultaneously. H4 tails partake in attractive cis and repulsive trans interactions at low [Mg(2+)]. These interactions are diminished at higher [Mg(2+)]. Simultaneous H3 and H4 tail truncation inhibited array oligomerization but maintained local array compaction at relatively high [Mg(2+)]. The established experimental approach can be extended to study the detailed molecular interactions mediated by epigenetic modification of flexible histone tails.
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Affiliation(s)
- Nathan P Nurse
- School of Chemical Engineering, Purdue University, West Lafayette, IN, 47906
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47
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Maeshima K, Rogge R, Tamura S, Joti Y, Hikima T, Szerlong H, Krause C, Herman J, Seidel E, DeLuca J, Ishikawa T, Hansen JC. Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers. EMBO J 2016; 35:1115-32. [PMID: 27072995 PMCID: PMC4868957 DOI: 10.15252/embj.201592660] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 03/08/2016] [Indexed: 11/10/2022] Open
Abstract
The existence of a 30‐nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular structures formed by reversible Mg2+‐dependent self‐association of linear 12‐mer nucleosomal arrays using microscopy and physicochemical approaches. These reconstituted chromatin structures, which we call “oligomers”, are globular throughout all stages of cooperative assembly and range in size from ~50 nm to a maximum diameter of ~1,000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10‐nm fibers, rather than folded 30‐nm structures. Linker DNA was freely accessible to micrococcal nuclease, although the oligomers remained partially intact after linker DNA digestion. The organization of chromosomal fibers in human nuclei in situ was stabilized by 1 mM MgCl2, but became disrupted in the absence of MgCl2, conditions that also dissociated the oligomers in vitro. These results indicate that a 10‐nm array of nucleosomes has the intrinsic ability to self‐assemble into large chromatin globules stabilized by nucleosome–nucleosome interactions, and suggest that the oligomers are a good in vitro model for investigating the structure and organization of interphase chromosomes.
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Affiliation(s)
- Kazuhiro Maeshima
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Japan
| | - Ryan Rogge
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Sachiko Tamura
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Japan XFEL Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI), Sayo-gun, Japan
| | | | - Heather Szerlong
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Christine Krause
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jake Herman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Erik Seidel
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
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48
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Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H. Structure and function of human histone H3.Y nucleosome. Nucleic Acids Res 2016; 44:6127-41. [PMID: 27016736 PMCID: PMC5291245 DOI: 10.1093/nar/gkw202] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
Histone H3.Y is a primate-specific, distant H3 variant. It is evolutionarily derived from H3.3, and may function in transcription regulation. However, the mechanism by which H3.Y regulates transcription has not been elucidated. In the present study, we determined the crystal structure of the H3.Y nucleosome, and found that many H3.Y-specific residues are located on the entry/exit sites of the nucleosome. Biochemical analyses revealed that the DNA ends of the H3.Y nucleosome were more flexible than those of the H3.3 nucleosome, although the H3.Y nucleosome was stable in vitro and in vivo. Interestingly, the linker histone H1, which compacts nucleosomal DNA, appears to bind to the H3.Y nucleosome less efficiently, as compared to the H3.3 nucleosome. These characteristics of the H3.Y nucleosome are also conserved in the H3.Y/H3.3 heterotypic nucleosome, which may be the predominant form in cells. In human cells, H3.Y preferentially accumulated around transcription start sites (TSSs). Taken together, H3.Y-containing nucleosomes around transcription start sites may form relaxed chromatin that allows transcription factor access, to regulate the transcription status of specific genes.
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Affiliation(s)
- Tomoya Kujirai
- 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
- Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shinichi Machida
- 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
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, 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 Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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49
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Krajewski WA. On the role of inter-nucleosomal interactions and intrinsic nucleosome dynamics in chromatin function. Biochem Biophys Rep 2016; 5:492-501. [PMID: 28955857 PMCID: PMC5600426 DOI: 10.1016/j.bbrep.2016.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/05/2016] [Accepted: 02/15/2016] [Indexed: 01/10/2023] Open
Abstract
Evidence is emerging that many diseases result from defects in gene functions, which, in turn, depend on the local chromatin environment of a gene. However, it still remains not fully clear how chromatin activity code is 'translated' to the particular 'activating' or 'repressing' chromatin structural transition. Commonly, chromatin remodeling in vitro was studied using mononucleosomes as a model. However, recent data suggest that structural reorganization of a single mononucleosome is not equal to remodeling of a nucleosome particle under multinucleosomal content - such as, interaction of nucleosomes via flexible histone termini could significantly alter the mode (and the resulting products) of nucleosome structural transitions. It is becoming evident that a nucleosome array does not constitute just a 'polymer' of individual 'canonical' nucleosomes due to multiple inter-nucleosomal interactions which affect nucleosome dynamics and structure. It could be hypothesized, that inter-nucleosomal interactions could act in cooperation with nucleosome inherent dynamics to orchestrate DNA-based processes and promote formation and stabilization of highly-dynamic, accessible structure of a nucleosome array. In the proposed paper we would like to discuss the nucleosome dynamics within the chromatin fiber mainly as it pertains to the roles of the structural changes mediated by inter-nucleosomal interactions.
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Affiliation(s)
- Wladyslaw A Krajewski
- Institute of Developmental Biology of Russian Academy of Sciences, ul. Vavilova 26, Moscow, 119334 Russia
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Nazarov I, Chekliarova I, Rychkov G, Ilatovskiy AV, Crane-Robinson C, Tomilin A. AFM studies in diverse ionic environments of nucleosomes reconstituted on the 601 positioning sequence. Biochimie 2015; 121:5-12. [PMID: 26586109 DOI: 10.1016/j.biochi.2015.11.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/09/2015] [Indexed: 01/02/2023]
Abstract
Atomic force microscopy (AFM) was used to study mononucleosomes reconstituted from a DNA duplex of 353 bp containing the strong 601 octamer positioning sequence, together with recombinant human core histone octamers. Three parameters were measured: 1) the length of DNA wrapped around the core histones; 2) the number of superhelical turns, calculated from the total angle through which the DNA is bent, and 3) the volume of the DNA-histone core. This approach allowed us to define in detail the structural diversity of nucleosomes caused by disassembly of the octasome to form subnucleosomal structures containing hexasomes, tetrasomes and disomes. At low ionic strength (TE buffer) and in the presence of physiological concentrations of monovalent cations, the majority of the particles were subnucleosomal, but physiological concentrations of bivalent cations resulted in about half of the nucleosomes being canonical octasomes in which the exiting DNA duplexes cross orthogonally. The dominance of this last species explains why bivalent but not monovalent cations can induce the initial step towards compaction and convergence of neighboring nucleosomes in nucleosomal arrays to form the chromatin fiber in the absence of linker histone. The observed nucleosome structural diversity may reflect the functional plasticity of nucleosomes under physiological conditions.
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Affiliation(s)
- Igor Nazarov
- Institute of Cytology, RAS, Tikhoretski Ave. 4, Saint-Petersburg, RF, 194064, Russia.
| | - Iana Chekliarova
- Institute of Cytology, RAS, Tikhoretski Ave. 4, Saint-Petersburg, RF, 194064, Russia
| | - Georgy Rychkov
- Institute of Physics, Nanotechnology and Telecommunications, NRU Peter the Great St.Petersburg Polytechnic University, Polytechnicheskaya 29, Saint-Petersburg, RF, 195251, Russia; Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, NRC "Kurchatov Institute", Orlova Roscha, Gatchina, 188300, Russia
| | - Andrey V Ilatovskiy
- Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute, NRC "Kurchatov Institute", Orlova Roscha, Gatchina, 188300, Russia; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Colyn Crane-Robinson
- Biophysics Laboratories, St. Michael's Building, University of Portsmouth, Portsmouth, PO1 2DT, UK
| | - Alexey Tomilin
- Institute of Cytology, RAS, Tikhoretski Ave. 4, Saint-Petersburg, RF, 194064, Russia
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