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Contribution of smFRET to Chromatin Research. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Chromatins are structural components of chromosomes and consist of DNA and histone proteins. The structure, dynamics, and function of chromatins are important in regulating genetic processes. Several different experimental and theoretical tools have been employed to understand chromatins better. In this review, we will focus on the literatures engrossed in understanding of chromatins using single-molecule Förster resonance energy transfer (smFRET). smFRET is a single-molecule fluorescence microscopic technique that can furnish information regarding the distance between two points in space. This has been utilized to efficiently unveil the structural details of chromatins.
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Sefer A, Kallis E, Eilert T, Röcker C, Kolesnikova O, Neuhaus D, Eustermann S, Michaelis J. Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level. Nat Commun 2022; 13:6569. [PMID: 36323657 PMCID: PMC9630430 DOI: 10.1038/s41467-022-34148-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1's multi-domain organization. Here, we directly probe this process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1's N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state.
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Affiliation(s)
- Anna Sefer
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Eleni Kallis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Tobias Eilert
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Boehringer Ingelheim, CoC CMC Statistics & Data Science, Birkendorfer Str. 65, 88400, Biberach, Germany
| | - Carlheinz Röcker
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Olga Kolesnikova
- European Molecular Biology Laboratory (EMBL), Heidelberg Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Sebastian Eustermann
- European Molecular Biology Laboratory (EMBL), Heidelberg Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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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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Zorro Shahidian L, Haas M, Le Gras S, Nitsch S, Mourão A, Geerlof A, Margueron R, Michaelis J, Daujat S, Schneider R. Succinylation of H3K122 destabilizes nucleosomes and enhances transcription. EMBO Rep 2021; 22:e51009. [PMID: 33512761 PMCID: PMC7926236 DOI: 10.15252/embr.202051009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/25/2022] Open
Abstract
Histone post-translational modifications (PTMs) are key players in chromatin regulation. The identification of novel histone acylations raises important questions regarding their role in transcription. In this study, we characterize the role of an acylation on the lateral surface of the histone octamer, H3K122 succinylation (H3K122succ), in chromatin function and transcription. Using chromatin succinylated at H3K122 in in vitro transcription assays, we show that the presence of H3K122succ is sufficient to stimulate transcription. In line with this, we found in our ChIP assays H3K122succ enriched on promoters of active genes and H3K122succ enrichment scaling with gene expression levels. Furthermore, we show that the co-activators p300/CBP can succinylate H3K122 and identify sirtuin 5 (SIRT5) as a new desuccinylase. By applying single molecule FRET assays, we demonstrate a direct effect of H3K122succ on nucleosome stability, indicating an important role for histone succinylation in modulating chromatin dynamics. Together, these data provide the first insights into the mechanisms underlying transcriptional regulation by H3K122succ.
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Affiliation(s)
| | | | - Stephanie Le Gras
- IGBMC, CNRS UMR7104, Inserm U1258Université de StrasbourgIllkirchFrance
- Plateforme GenomEastInfrastructure France GénomiqueCedexFrance
| | - Sandra Nitsch
- Institute of Functional EpigeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - André Mourão
- Protein Expression and Purification FacilityHelmholtz Zentrum MünchenNeuherbergGermany
| | - Arie Geerlof
- Protein Expression and Purification FacilityHelmholtz Zentrum MünchenNeuherbergGermany
| | | | | | - Sylvain Daujat
- IGBMC, CNRS UMR7104, Inserm U1258Université de StrasbourgIllkirchFrance
- Present address:
Biotechnology and Cell SignalingCNRS UMR7242University of StrasbourgCedexFrance
| | - Robert Schneider
- Institute of Functional EpigeneticsHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- Faculty of BiologyLudwig‐Maximilians Universität MünchenPlanegg‐MartinsriedGermany
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Ghoneim M, Fuchs HA, Musselman CA. Histone Tail Conformations: A Fuzzy Affair with DNA. Trends Biochem Sci 2021; 46:564-578. [PMID: 33551235 DOI: 10.1016/j.tibs.2020.12.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022]
Abstract
The core histone tails are critical in chromatin structure and signaling. Studies over the past several decades have provided a wealth of information on the histone tails and their interaction with chromatin factors. However, the conformation of the histone tails in a chromatin relevant context has remained elusive. Only recently has enough evidence emerged to start to build a structural model of the tails in the context of nucleosomes and nucleosome arrays. Here, we review these studies and propose that the histone tails adopt a high-affinity fuzzy complex with DNA, characterized by robust but dynamic association. Furthermore, we discuss how these DNA-bound conformational ensembles promote distinct chromatin structure and signaling, and that their fuzzy nature is important in transitioning between functional states.
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Affiliation(s)
- Mohamed Ghoneim
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Harrison A Fuchs
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Catherine A Musselman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Willhoft O, Wigley DB. INO80 and SWR1 complexes: the non-identical twins of chromatin remodelling. Curr Opin Struct Biol 2020; 61:50-58. [PMID: 31838293 PMCID: PMC7171469 DOI: 10.1016/j.sbi.2019.09.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/07/2019] [Indexed: 02/06/2023]
Abstract
The INO80 family of chromatin remodellers are multisubunit complexes that perform a variety of tasks on nucleosomes. Family members are built around a heterohexamer of RuvB-like protein, an ATP-dependent DNA translocase,nuclear actin and actin-related proteins, and a few complex-specific subunits. They modify chromatin in a number of ways including nucleosome sliding and exchange of variant histones. Recent structural information on INO80 and SWR1 complexes has revealed similarities in the basic architecture of the complexes. However, structural and biochemical data on the complexes bound to nucleosomes reveal these similarities to be somewhat superficial and their biochemical activities and mechanisms are very different. Consequently, the INO80 family displays a surprising diversity of function that is based upon a similar structural framework.
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Affiliation(s)
- Oliver Willhoft
- Section of Structural and Synthetic Biology, Dept. Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Dale B Wigley
- Section of Structural and Synthetic Biology, Dept. Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
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Zhou K, Gaullier G, Luger K. Nucleosome structure and dynamics are coming of age. Nat Struct Mol Biol 2018; 26:3-13. [PMID: 30532059 DOI: 10.1038/s41594-018-0166-x] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022]
Abstract
Since the first high-resolution structure of the nucleosome was reported in 1997, the available information on chromatin structure has increased very rapidly. Here, we review insights derived from cutting-edge biophysical and structural approaches applied to the study of nucleosome dynamics and nucleosome-binding factors, with a focus on the experimental advances driving the research. In addition, we highlight emerging challenges in nucleosome structural biology.
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Affiliation(s)
- Keda Zhou
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Guillaume Gaullier
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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Weaver TM, Morrison EA, Musselman CA. Reading More than Histones: The Prevalence of Nucleic Acid Binding among Reader Domains. Molecules 2018; 23:molecules23102614. [PMID: 30322003 PMCID: PMC6222470 DOI: 10.3390/molecules23102614] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 01/09/2023] Open
Abstract
The eukaryotic genome is packaged into the cell nucleus in the form of chromatin, a complex of genomic DNA and histone proteins. Chromatin structure regulation is critical for all DNA templated processes and involves, among many things, extensive post-translational modification of the histone proteins. These modifications can be “read out” by histone binding subdomains known as histone reader domains. A large number of reader domains have been identified and found to selectively recognize an array of histone post-translational modifications in order to target, retain, or regulate chromatin-modifying and remodeling complexes at their substrates. Interestingly, an increasing number of these histone reader domains are being identified as also harboring nucleic acid binding activity. In this review, we present a summary of the histone reader domains currently known to bind nucleic acids, with a focus on the molecular mechanisms of binding and the interplay between DNA and histone recognition. Additionally, we highlight the functional implications of nucleic acid binding in chromatin association and regulation. We propose that nucleic acid binding is as functionally important as histone binding, and that a significant portion of the as yet untested reader domains will emerge to have nucleic acid binding capabilities.
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Affiliation(s)
- Tyler M Weaver
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling. Nat Struct Mol Biol 2018; 25:823-832. [PMID: 30177756 DOI: 10.1038/s41594-018-0115-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2022]
Abstract
Nuclear actin (N-actin) and actin-related proteins (Arps) are critical components of several chromatin modulating complexes, including the chromatin remodeler INO80, but their function is largely elusive. Here, we report the crystal structure of the 180-kDa Arp8 module of Saccharomyces cerevisiae INO80 and establish its role in recognition of extranucleosomal linker DNA. Arp8 engages N-actin in a manner distinct from that of other actin-fold proteins and thereby specifies recruitment of the Arp4-N-actin heterodimer to a segmented scaffold of the helicase-SANT-associated (HSA) domain of Ino80. The helical HSA domain spans over 120 Å and provides an extended binding platform for extranucleosomal entry DNA that is required for nucleosome sliding and genome-wide nucleosome positioning. Together with the recent cryo-electron microscopy structure of INO80Core-nucleosome complex, our findings suggest an allosteric mechanism by which INO80 senses 40-bp linker DNA to conduct highly processive chromatin remodeling.
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SUN LL, SU YY, GAO YJ, Li W, LYU H, LI B, LI D. Progresses of Single Molecular Fluorescence Resonance Energy Transfer in Studying Biomacromolecule Dynamic Process. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61088-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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