1
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Onoa B, Díaz-Celis C, Cañari-Chumpitaz C, Lee A, Bustamante C. Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy. ACS CENTRAL SCIENCE 2024; 10:122-137. [PMID: 38292612 PMCID: PMC10823521 DOI: 10.1021/acscentsci.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/30/2023] [Accepted: 11/30/2023] [Indexed: 02/01/2024]
Abstract
During replication, expression, and repair of the eukaryotic genome, cellular machinery must access the DNA wrapped around histone proteins forming nucleosomes. These octameric protein·DNA complexes are modular, dynamic, and flexible and unwrap or disassemble either spontaneously or by the action of molecular motors. Thus, the mechanism of formation and regulation of subnucleosomal intermediates has gained attention genome-wide because it controls DNA accessibility. Here, we imaged nucleosomes and their more compacted structure with the linker histone H1 (chromatosomes) using high-speed atomic force microscopy to visualize simultaneously the changes in the DNA and the histone core during their disassembly when deposited on mica. Furthermore, we trained a neural network and developed an automatic algorithm to track molecular structural changes in real time. Our results show that nucleosome disassembly is a sequential process involving asymmetrical stepwise dimer ejection events. The presence of H1 restricts DNA unwrapping, significantly increases the nucleosomal lifetime, and affects the pathway in which heterodimer asymmetrical dissociation occurs. We observe that tetrasomes are resilient to disassembly and that the tetramer core (H3·H4)2 can diffuse along the nucleosome positioning sequence. Tetrasome mobility might be critical to the proper assembly of nucleosomes and can be relevant during nucleosomal transcription, as tetrasomes survive RNA polymerase passage. These findings are relevant to understanding nucleosome intrinsic dynamics and their modification by DNA-processing enzymes.
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Affiliation(s)
- Bibiana Onoa
- Jason
L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
| | - César Díaz-Celis
- Jason
L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
| | - Cristhian Cañari-Chumpitaz
- Jason
L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
| | - Antony Lee
- Laboratoire
Photonique Numérique et Nanosciences, LP2N UMR 5298, Université de Bordeaux, Institut d’Optique,
CNRS, F-33400 Talence, France
| | - Carlos Bustamante
- Jason
L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of
California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Kavli
Energy Nanoscience Institute, University
of California, Berkeley, California 94720, United States
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2
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Li S, Wei T, Panchenko AR. Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility. Nat Commun 2023; 14:769. [PMID: 36765119 PMCID: PMC9918499 DOI: 10.1038/s41467-023-36465-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
Nucleosomes, containing histone variants H2A.Z, are important for gene transcription initiation and termination, chromosome segregation and DNA double-strand break repair, among other functions. However, the underlying mechanisms of how H2A.Z influences nucleosome stability, dynamics and DNA accessibility are not well understood, as experimental and computational evidence remains inconclusive. Our modeling efforts of human nucleosome stability and dynamics, along with comparisons with experimental data show that the incorporation of H2A.Z results in a substantial decrease of the energy barrier for DNA unwrapping. This leads to the spontaneous DNA unwrapping of about forty base pairs from both ends, nucleosome gapping and increased histone plasticity, which otherwise is not observed for canonical nucleosomes. We demonstrate that both N- and C-terminal tails of H2A.Z play major roles in these events, whereas the H3.3 variant exerts a negligible impact in modulating the DNA end unwrapping. In summary, our results indicate that H2A.Z deposition makes nucleosomes more mobile and DNA more accessible to transcriptional machinery and other chromatin components.
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Affiliation(s)
- Shuxiang Li
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Tiejun Wei
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada. .,Department of Biology and Molecular Sciences, Queen's University, Kingston, ON, Canada. .,School of Computing, Queen's University, Kingston, ON, Canada. .,Ontario Institute of Cancer Research, Toronto, Canada.
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3
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Johnson SL, Narlikar GJ. ATP hydrolysis coordinates the activities of two motors in a dimeric chromatin remodeling enzyme. J Mol Biol 2022; 434:167653. [PMID: 35659534 DOI: 10.1016/j.jmb.2022.167653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/12/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Abstract
ATP-dependent chromatin remodelers are essential enzymes that restructure eukaryotic genomes to enable all DNA-based processes. The diversity and complexity of these processes are matched by the complexity of the enzymes that carry them out, making remodelers a challenging class of molecular motors to study by conventional methods. Here we use a single molecule biophysical assay to overcome some of these challenges, enabling a detailed mechanistic dissection of a paradigmatic remodeler reaction, that of sliding a nucleosome towards the longer DNA linker. We focus on how two motors of a dimeric remodeler coordinate to accomplish such directional sliding. We find that ATP hydrolysis by both motors promotes coordination, suggesting a role for ATP in resolving the competition for directional commitment. Furthermore, we show an artificially constitutive dimer is no more or less coordinated, but is more processive, suggesting a cell could modulate a remodeler's oligomeric state to modulate local chromatin dynamics.
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Affiliation(s)
- Stephanie L Johnson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA. https://twitter.com/StephL_Johnson
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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4
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Determining translocation orientations of nucleic acid helicases. Methods 2021; 204:160-171. [PMID: 34758393 PMCID: PMC9076756 DOI: 10.1016/j.ymeth.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Helicase enzymes translocate along an RNA or DNA template with a defined polarity to unwind, separate, or remodel duplex strands for a variety of genome maintenance processes. Helicase mutations are commonly associated with a variety of diseases including aging, cancer, and neurodegeneration. Biochemical characterization of these enzymes has provided a wealth of information on the kinetics of unwinding and substrate preferences, and several high-resolution structures of helicases alone and bound to oligonucleotides have been solved. Together, they provide mechanistic insights into the structural translocation and unwinding orientations of helicases. However, these insights rely on structural inferences derived from static snapshots. Instead, continued efforts should be made to combine structure and kinetics to better define active translocation orientations of helicases. This review explores many of the biochemical and biophysical methods utilized to map helicase binding orientation to DNA or RNA substrates and includes several time-dependent methods to unequivocally map the active translocation orientation of these enzymes to better define the active leading and trailing faces.
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5
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Casari E, Gobbini E, Gnugnoli M, Mangiagalli M, Clerici M, Longhese MP. Dpb4 promotes resection of DNA double-strand breaks and checkpoint activation by acting in two different protein complexes. Nat Commun 2021; 12:4750. [PMID: 34362907 PMCID: PMC8346560 DOI: 10.1038/s41467-021-25090-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 07/20/2021] [Indexed: 12/24/2022] Open
Abstract
Budding yeast Dpb4 (POLE3/CHRAC17 in mammals) is a highly conserved histone fold protein that is shared by two protein complexes: the chromatin remodeler ISW2/hCHRAC and the DNA polymerase ε (Pol ε) holoenzyme. In Saccharomyces cerevisiae, Dpb4 forms histone-like dimers with Dls1 in the ISW2 complex and with Dpb3 in the Pol ε complex. Here, we show that Dpb4 plays two functions in sensing and processing DNA double-strand breaks (DSBs). Dpb4 promotes histone removal and DSB resection by interacting with Dls1 to facilitate the association of the Isw2 ATPase to DSBs. Furthermore, it promotes checkpoint activation by interacting with Dpb3 to facilitate the association of the checkpoint protein Rad9 to DSBs. Persistence of both Isw2 and Rad9 at DSBs is enhanced by the A62S mutation that is located in the Dpb4 histone fold domain and increases Dpb4 association at DSBs. Thus, Dpb4 exerts two distinct functions at DSBs depending on its interactors. The histone folding protein Dpb4 forms histone-like dimers within the ISW2 complex and the Pol ε complex in S. cerevisiae. Here the authors reveal insights into two distinct functions that Dpb4 exerts at DSBs depending on its interactors.
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Affiliation(s)
- Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Marco Gnugnoli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Marco Mangiagalli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy.
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6
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Gamarra N, Narlikar GJ. Histone dynamics play a critical role in SNF2h-mediated nucleosome sliding. Nat Struct Mol Biol 2021; 28:548-551. [PMID: 34226739 PMCID: PMC9040563 DOI: 10.1038/s41594-021-00620-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nathan Gamarra
- Department of Biochemistry and Biophysics, University of
California, San Francisco, San Francisco, United States,TETRAD Graduate Program, University of California, San
Francisco, San Francisco, United States
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of
California, San Francisco, San Francisco, United States,Corresponding author:
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7
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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8
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Histone dynamics mediate DNA unwrapping and sliding in nucleosomes. Nat Commun 2021; 12:2387. [PMID: 33888707 PMCID: PMC8062685 DOI: 10.1038/s41467-021-22636-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly wrap ∼147 DNA base pairs around an octamer of histone proteins. How nucleosome structural dynamics affect genome functioning is not completely clear. Here we report all-atom molecular dynamics simulations of nucleosome core particles at a timescale of 15 microseconds. At this timescale, functional modes of nucleosome dynamics such as spontaneous nucleosomal DNA breathing, unwrapping, twisting, and sliding were observed. We identified atomistic mechanisms of these processes by analyzing the accompanying structural rearrangements of the histone octamer and histone-DNA contacts. Octamer dynamics and plasticity were found to enable DNA unwrapping and sliding. Through multi-scale modeling, we showed that nucleosomal DNA dynamics contribute to significant conformational variability of the chromatin fiber at the supranucleosomal level. Our study further supports mechanistic coupling between fine details of histone dynamics and chromatin functioning, provides a framework for understanding the effects of various chromatin modifications.
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9
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Doğan D, Arslan M, Uluçay T, Kalyoncu S, Dimitrov S, Kale S. CENP-A Nucleosome is a Sensitive Allosteric Scaffold for DNA and Chromatin Factors. J Mol Biol 2020; 433:166789. [PMID: 33387534 DOI: 10.1016/j.jmb.2020.166789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/06/2020] [Accepted: 12/18/2020] [Indexed: 02/02/2023]
Abstract
Centromeric loci of chromosomes are defined by nucleosomes containing the histone H3 variant CENP-A, which bind their DNA termini more permissively than their canonical counterpart, a feature that is critical for the mitotic fidelity. A recent cryo-EM study demonstrated that the DNA termini of CENP-A nucleosomes, reconstituted with the Widom 601 DNA sequence, are asymmetrically flexible, meaning one terminus is more clearly resolved than the other. However, an earlier work claimed that both ends could be resolved in the presence of two stabilizing single chain variable fragment (scFv) antibodies per nucleosome, and thus are likely permanently bound to the histone octamer. This suggests that the binding of scFv antibodies to the histone octamer surface would be associated with CENP-A nucleosome conformational changes, including stable binding of the DNA termini. Here, we present computational evidence that allows to explain at atomistic level the structural rearrangements of CENP-A nucleosomes resulting from the antibody binding. The antibodies, while they only bind the octamer façades, are capable of altering the dynamics of the nucleosomal core, and indirectly also the surrounding DNA. This effect has more drastic implications for the structure and the dynamics of the CENP-A nucleosome in comparison to its canonical counterpart. Furthermore, we find evidence that the antibodies bind the left and the right octamer façades at different affinities, another manifestation of the DNA sequence. We speculate that the cells could use induction of similar allosteric effects to control centromere function.
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Affiliation(s)
- Deniz Doğan
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey
| | - Merve Arslan
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey
| | - Tuğçe Uluçay
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey
| | - Sibel Kalyoncu
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey; Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey.
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10
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Morgan A, LeGresley S, Fischer C. Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability. Int J Mol Sci 2020; 22:ijms22010076. [PMID: 33374740 PMCID: PMC7793527 DOI: 10.3390/ijms22010076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.
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11
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Huertas J, Cojocaru V. Breaths, Twists, and Turns of Atomistic Nucleosomes. J Mol Biol 2020; 433:166744. [PMID: 33309853 DOI: 10.1016/j.jmb.2020.166744] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023]
Abstract
Gene regulation programs establish cellular identity and rely on dynamic changes in the structural packaging of genomic DNA. The DNA is packaged in chromatin, which is formed from arrays of nucleosomes displaying different degree of compaction and different lengths of inter-nucleosomal linker DNA. The nucleosome represents the repetitive unit of chromatin and is formed by wrapping 145-147 basepairs of DNA around an octamer of histone proteins. Each of the four histones is present twice and has a structured core and intrinsically disordered terminal tails. Chromatin dynamics are triggered by inter- and intra-nucleosome motions that are controlled by the DNA sequence, the interactions between the histone core and the DNA, and the conformations, positions, and DNA interactions of the histone tails. Understanding chromatin dynamics requires studying all these features at the highest possible resolution. For this, molecular dynamics simulations can be used as a powerful complement or alternative to experimental approaches, from which it is often very challenging to characterize the structural features and atomic interactions controlling nucleosome motions. Molecular dynamics simulations can be performed at different resolutions, by coarse graining the molecular system with varying levels of details. Here we review the successes and the remaining challenges of the application of atomic resolution simulations to study the structure and dynamics of nucleosomes and their complexes with interacting partners.
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Affiliation(s)
- Jan Huertas
- In Silico Biomolecular Structure and Dynamics Group, Hubrecht Institute, Utrecht, the Netherlands; Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany
| | - Vlad Cojocaru
- In Silico Biomolecular Structure and Dynamics Group, Hubrecht Institute, Utrecht, the Netherlands; Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany; Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster, Germany.
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12
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Bhardwaj SK, Hailu SG, Olufemi L, Brahma S, Kundu S, Hota SK, Persinger J, Bartholomew B. Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation. Nat Commun 2020; 11:5913. [PMID: 33219211 PMCID: PMC7680125 DOI: 10.1038/s41467-020-19700-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA. By mutational analysis and uncoupling of ISW1a's dinucleosome specificity, we find that dinucleosome recognition is required by ISW1a for proper chromatin organization at promoters; as well as transcription regulation in combination with the histone acetyltransferase NuA4 and histone H2A.Z exchanger SWR1.
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Affiliation(s)
- Saurabh K Bhardwaj
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- Worldwide Research and Development, Pfizer Inc, Houston, USA
| | - Solomon G Hailu
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- EpiCypher, Inc., Durham, USA
| | - Lola Olufemi
- National Institute of Neurological Disorders and Stroke, Bethesda, USA
| | - Sandipan Brahma
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, USA
| | - Soumyadipta Kundu
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- ZS Associates, Evanston, USA
| | - Swetansu K Hota
- University of California-San Francisco, Gladstone Institutes, San Francisco, USA
| | - Jim Persinger
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
| | - Blaine Bartholomew
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA.
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA.
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13
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Takada S, Brandani GB, Tan C. Nucleosomes as allosteric scaffolds for genetic regulation. Curr Opin Struct Biol 2020; 62:93-101. [PMID: 31901887 DOI: 10.1016/j.sbi.2019.11.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022]
Abstract
Nucleosomes are stable yet highly dynamic complexes exhibiting diverse types of motions, such as sliding, DNA unwrapping, and disassembly, encoding a landscape with a large number of metastable states. In this review, describing recent studies on these nucleosome structure changes, we propose that the nucleosome can be viewed as an ideal allosteric scaffold: regulated by effector molecules such as transcription factors and chromatin remodelers, the nucleosome controls the downstream gene activity. Binding of transcription factors to the nucleosome can enhance DNA unwrapping or slide the DNA, altering either the binding or the unbinding of other transcription factors to nearby sites. ATP-dependent chromatin remodelers induce a series of DNA deformations, which allosterically propagate throughout the nucleosome to induce DNA sliding or histone exchange.
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Affiliation(s)
- Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo Kyoto, 606-8502, Japan.
| | - Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo Kyoto, 606-8502, Japan
| | - Cheng Tan
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo, Kobe, 650-0047 Japan
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14
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Affiliation(s)
- Jean-Paul Armache
- Department of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yifan Cheng
- Howard Hughes Medical Institute, University of California San Francisco, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, USA
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