1
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Kim JM, Carcamo CC, Jazani S, Xie Z, Feng XA, Yamadi M, Poyton M, Holland KL, Grimm JB, Lavis LD, Ha T, Wu C. Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers. eLife 2024; 12:RP91433. [PMID: 38497611 PMCID: PMC10948146 DOI: 10.7554/elife.91433] [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: 03/19/2024] Open
Abstract
Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement, and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and two-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding, respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/s on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Claudia C Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Sina Jazani
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Zepei Xie
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xinyu A Feng
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Maryam Yamadi
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Matthew Poyton
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Katie L Holland
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
- Howard Hughes Medical InstituteBostonUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins School of MedicineBaltimoreUnited States
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2
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Sabantsev A, Deindl S. The voyage is as important as the harbor. eLife 2024; 13:e96836. [PMID: 38488335 PMCID: PMC10942777 DOI: 10.7554/elife.96836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
To find nucleosomes, chromatin remodelers slide and hop along DNA, and their direction of approach affects the direction that nucleosomes slide in.
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Affiliation(s)
- Anton Sabantsev
- Department of Cell and Molecular Biology, Uppsala UniversityUppsalaSweden
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Uppsala UniversityUppsalaSweden
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3
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Kim JM, Carcamo CC, Jazani S, Xie Z, Feng XA, Yamadi M, Poyton M, Holland KL, Grimm JB, Lavis LD, Ha T, Wu C. Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.13.544671. [PMID: 38293098 PMCID: PMC10827135 DOI: 10.1101/2023.06.13.544671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/sec on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Claudia C. Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sina Jazani
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zepei Xie
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xinyu A. Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maryam Yamadi
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Poyton
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Katie L. Holland
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
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4
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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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5
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Yang C, Dong X, Ma Z, Li B, Bi C, Zhang X. Pioneer Factor Improves CRISPR-Based C-To-G and C-To-T Base Editing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202957. [PMID: 35861371 PMCID: PMC9475549 DOI: 10.1002/advs.202202957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 05/13/2023]
Abstract
Base editing events in eukaryote require a compatible chromatin environment, but there is little research on how chromatin factors contribute to the editing efficiency or window. By engineering BEs (base editors) fused with various pioneer factors, the authors found that SOX2 substantially increased the editing efficiency for GBE and CBE. While SoxN-GBE (SOX2-NH3-GBE) improved the editing efficiency at overall cytosines of the protospacer, SoxM-GBE/CBE (SOX2-Middle-GBE/CBE) enabled the higher base editing at PAM-proximal cytosines. By separating functional domains of SOX2, the SadN-GBE (SOX2 activation domain-NH3-GBE) is constructed for higher editing efficiency and SadM-CBE for broader editing window to date. With the DNase I assay, it is also proved the increased editing efficiency is most likely associated with the induction of chromatin accessibility by SAD. Finally, SadM-CBE is employed to introduce a stop codon in the proto-oncogene MYC, at a locus rarely edited by previous editors with high efficiency. In this work, a new class of pioneer-BEs is constructed by fusion of pioneer factor or its functional domains, which exhibits higher editing efficiency or broader editing window in eukaryote.
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Affiliation(s)
- Chao Yang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Xingxiao Dong
- School of Biological EngineeringDalian Polytechnic UniversityDalian116034China
| | - Zhenzhen Ma
- College of Life SciencesNankai UniversityTianjin300071China
| | - Bo Li
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Changhao Bi
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Xueli Zhang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
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6
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Hsieh LJ, Gourdet MA, Moore CM, Muñoz EN, Gamarra N, Ramani V, Narlikar GJ. A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Mol Cell 2022; 82:2098-2112.e4. [PMID: 35597239 PMCID: PMC9351570 DOI: 10.1016/j.molcel.2022.04.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 12/10/2021] [Accepted: 04/20/2022] [Indexed: 10/18/2022]
Abstract
The critical role of the INO80 chromatin remodeling complex in transcription is commonly attributed to its nucleosome sliding activity. Here, we have found that INO80 prefers to mobilize hexasomes over nucleosomes. INO80's preference for hexasomes reaches up to ∼60 fold when flanking DNA overhangs approach ∼18-bp linkers in yeast gene bodies. Correspondingly, deletion of INO80 significantly affects the positions of hexasome-sized particles within yeast genes in vivo. Our results raise the possibility that INO80 promotes nucleosome sliding by dislodging an H2A-H2B dimer, thereby making a nucleosome transiently resemble a hexasome. We propose that this mechanism allows INO80 to rapidly mobilize nucleosomes at promoters and hexasomes within gene bodies. Rapid repositioning of hexasomes that are generated in the wake of transcription may mitigate spurious transcription. More generally, such versatility may explain how INO80 regulates chromatin architecture during the diverse processes of transcription, replication, and repair.
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Affiliation(s)
- Laura J Hsieh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Muryam A Gourdet
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Camille M Moore
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elise N Muñoz
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Vijay Ramani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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7
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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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8
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Acidic patch histone mutations and their effects on nucleosome remodeling. Biochem Soc Trans 2022; 50:907-919. [PMID: 35356970 DOI: 10.1042/bst20210773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 12/15/2022]
Abstract
Structural and biochemical studies have identified a histone surface on each side of the nucleosome disk termed 'the nucleosome acidic patch' that acts as a regulatory hub for the function of numerous nuclear proteins, including ATP-dependent chromatin complexes (remodelers). Four major remodeler subfamilies, SWI/SNF, ISWI, CHD, and INO80, have distinct modes of interaction with one or both nucleosome acidic patches, contributing to their specific remodeling outcomes. Genome-wide sequencing analyses of various human cancers have uncovered high-frequency mutations in histone coding genes, including some that map to the acidic patch. How cancer-related acidic patch histone mutations affect nucleosome remodeling is mainly unknown. Recent advances in in vitro chromatin reconstitution have enabled access to physiologically relevant nucleosomes, including asymmetric nucleosomes that possess both wild-type and acidic patch mutant histone copies. Biochemical investigation of these substrates revealed unexpected remodeling outcomes with far-reaching implications for alteration of chromatin structure. This review summarizes recent findings of how different remodeler families interpret wild-type and mutant acidic patches for their remodeling functions and discusses models for remodeler-mediated changes in chromatin landscapes as a consequence of acidic patch mutations.
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9
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Poyton MF, Feng XA, Ranjan A, Lei Q, Wang F, Zarb JS, Louder RK, Park G, Jo MH, Ye J, Liu S, Ha T, Wu C. Coordinated DNA and histone dynamics drive accurate histone H2A.Z exchange. SCIENCE ADVANCES 2022; 8:eabj5509. [PMID: 35263135 PMCID: PMC8906749 DOI: 10.1126/sciadv.abj5509] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Nucleosomal histone H2A is exchanged for its variant H2A.Z by the SWR1 chromatin remodeler, but the mechanism and timing of histone exchange remain unclear. Here, we quantify DNA and histone dynamics during histone exchange in real time using a three-color single-molecule FRET assay. We show that SWR1 operates with timed precision to unwrap DNA with large displacement from one face of the nucleosome, remove H2A-H2B from the same face, and rewrap DNA, all within 2.3 s. This productive DNA unwrapping requires full SWR1 activation and differs from unproductive, smaller-scale DNA unwrapping caused by SWR1 binding alone. On an asymmetrically positioned nucleosome, SWR1 intrinsically senses long-linker DNA to preferentially exchange H2A.Z on the distal face as observed in vivo. The displaced H2A-H2B dimer remains briefly associated with the SWR1-nucleosome complex and is dissociated by histone chaperones. These findings reveal how SWR1 coordinates DNA unwrapping with histone dynamics to rapidly and accurately place H2A.Z at physiological sites on chromatin.
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Affiliation(s)
- Matthew F. Poyton
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Xinyu A. Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Anand Ranjan
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Qin Lei
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Feng Wang
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jasmin S. Zarb
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Robert K. Louder
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Giho Park
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Myung Hyun Jo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joseph Ye
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sheng Liu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
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10
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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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11
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Schoberleitner I, Bauer I, Huang A, Andreyeva EN, Sebald J, Pascher K, Rieder D, Brunner M, Podhraski V, Oemer G, Cázarez-García D, Rieder L, Keller MA, Winkler R, Fyodorov DV, Lusser A. CHD1 controls H3.3 incorporation in adult brain chromatin to maintain metabolic homeostasis and normal lifespan. Cell Rep 2021; 37:109769. [PMID: 34610319 PMCID: PMC8607513 DOI: 10.1016/j.celrep.2021.109769] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 07/26/2021] [Accepted: 09/08/2021] [Indexed: 01/31/2023] Open
Abstract
The ATP-dependent chromatin remodeling factor CHD1 is essential for the assembly of variant histone H3.3 into paternal chromatin during sperm chromatin remodeling in fertilized eggs. It remains unclear, however, if CHD1 has a similar role in normal diploid cells. Using a specifically tailored quantitative mass spectrometry approach, we show that Chd1 disruption results in reduced H3.3 levels in heads of Chd1 mutant flies. Chd1 deletion perturbs brain chromatin structure in a similar way as H3.3 deletion and leads to global de-repression of transcription. The physiological consequences are reduced food intake, metabolic alterations, and shortened lifespan. Notably, brain-specific CHD1 expression rescues these phenotypes. We further demonstrate a strong genetic interaction between Chd1 and H3.3 chaperone Hira. Thus, our findings establish CHD1 as a factor required for the assembly of H3.3-containing chromatin in adult cells and suggest a crucial role for CHD1 in the brain as a regulator of organismal health and longevity.
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Affiliation(s)
- Ines Schoberleitner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Ingo Bauer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Anming Huang
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Evgeniya N Andreyeva
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Johanna Sebald
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Katharina Pascher
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Melanie Brunner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Valerie Podhraski
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Gregor Oemer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Daniel Cázarez-García
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato 36824, Mexico
| | - Leila Rieder
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Markus A Keller
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato 36824, Mexico
| | - Dmitry V Fyodorov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria.
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12
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Kim JM, Visanpattanasin P, Jou V, Liu S, Tang X, Zheng Q, Li KY, Snedeker J, Lavis LD, Lionnet T, Wu C. Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin. eLife 2021; 10:e69387. [PMID: 34313223 PMCID: PMC8352589 DOI: 10.7554/elife.69387] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending 'tug-of-war' that controls a temporally shifting window of accessibility for the transcription initiation machinery.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | | | - Vivian Jou
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Sheng Liu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xiaona Tang
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Kai Yu Li
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Jonathan Snedeker
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Timothee Lionnet
- Institute of Systems Genetics, Langone Medical Center, New York UniversityNew YorkUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins School of MedicineBaltimoreUnited States
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13
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Autoinhibitory elements of the Chd1 remodeler block initiation of twist defects by destabilizing the ATPase motor on the nucleosome. Proc Natl Acad Sci U S A 2021; 118:2014498118. [PMID: 33468676 DOI: 10.1073/pnas.2014498118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin remodelers are ATP (adenosine triphosphate)-powered motors that reposition nucleosomes throughout eukaryotic chromosomes. Remodelers possess autoinhibitory elements that control the direction of nucleosome sliding, but underlying mechanisms of inhibition have been unclear. Here, we show that autoinhibitory elements of the yeast Chd1 remodeler block nucleosome sliding by preventing initiation of twist defects. We show that two autoinhibitory elements-the chromodomains and bridge-reinforce each other to block sliding when the DNA-binding domain is not bound to entry-side DNA. Our data support a model where the chromodomains and bridge target nucleotide-free and ADP-bound states of the ATPase motor, favoring a partially disengaged state of the ATPase motor on the nucleosome. By bypassing distortions of nucleosomal DNA prior to ATP binding, we propose that autoinhibitory elements uncouple the ATP binding/hydrolysis cycle from DNA translocation around the histone core.
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14
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Morrison EA, Baweja L, Poirier MG, Wereszczynski J, Musselman CA. Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility. Nucleic Acids Res 2021; 49:4750-4767. [PMID: 33856458 PMCID: PMC8096233 DOI: 10.1093/nar/gkab246] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/07/2021] [Accepted: 03/28/2021] [Indexed: 01/30/2023] Open
Abstract
Hexasomes and tetrasomes are intermediates in nucleosome assembly and disassembly. Their formation is promoted by histone chaperones, ATP-dependent remodelers, and RNA polymerase II. In addition, hexasomes are maintained in transcribed genes and could be an important regulatory factor. While nucleosome composition has been shown to affect the structure and accessibility of DNA, its influence on histone tails is largely unknown. Here, we investigate the conformational dynamics of the H3 tail in the hexasome and tetrasome. Using a combination of NMR spectroscopy, MD simulations, and trypsin proteolysis, we find that the conformational ensemble of the H3 tail is regulated by nucleosome composition. As has been found for the nucleosome, the H3 tails bind robustly to DNA within the hexasome and tetrasome, but upon loss of the H2A/H2B dimer, we determined that the adjacent H3 tail has an altered conformational ensemble, increase in dynamics, and increase in accessibility. Similar to observations of DNA dynamics, this is seen to be asymmetric in the hexasome. Our results indicate that nucleosome composition has the potential to regulate chromatin signaling and ultimately help shape the chromatin landscape.
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Affiliation(s)
- Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Lokesh Baweja
- Department of Physics, Illinois Institute of Technology, Chicago, IL, USA
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, USA
| | - Michael G Poirier
- Department of Physics, Biophysics Graduate Program, Ohio State Biochemistry Graduate Program, and Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Jeff Wereszczynski
- Department of Physics, Illinois Institute of Technology, Chicago, IL, USA
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, USA
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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15
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Feng XA, Poyton MF, Ha T. Multicolor single-molecule FRET for DNA and RNA processes. Curr Opin Struct Biol 2021; 70:26-33. [PMID: 33894656 DOI: 10.1016/j.sbi.2021.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 12/31/2022]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is a useful tool for observing the dynamics of protein-nucleic acid interactions. Although most smFRET measurements have used two fluorophores, multicolor smFRET measurements using more than two fluorophores offer more information about how protein-nucleic acid complexes dynamically move, assemble, and disassemble. Multicolor smFRET experiments include three or more fluorophores and at least one donor-acceptor pair. This review highlights how multicolor smFRET is being used to probe the dynamics of three different classes of biochemical processes-protein-DNA interactions, chromatin remodeling, and protein translation.
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Affiliation(s)
- Xinyu A Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew F Poyton
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA; Howard Hughes Medical Institute, Baltimore, MD, USA.
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16
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Jiang Z, Zhang B. On the role of transcription in positioning nucleosomes. PLoS Comput Biol 2021; 17:e1008556. [PMID: 33417594 PMCID: PMC7819601 DOI: 10.1371/journal.pcbi.1008556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/21/2021] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Nucleosome positioning is crucial for the genome’s function. Though the role of DNA sequence in positioning nucleosomes is well understood, a detailed mechanistic understanding on the impact of transcription remains lacking. Using numerical simulations, we investigated the dependence of nucleosome density profiles on transcription level across multiple species. We found that the low nucleosome affinity of yeast, but not mouse, promoters contributes to the formation of phased nucleosomes arrays for inactive genes. For the active genes, a heterogeneous distribution of +1 nucleosomes, caused by a tug-of-war between two types of remodeling enzymes, is essential for reproducing their density profiles. In particular, while positioning enzymes are known to remodel the +1 nucleosome and align it toward the transcription start site (TSS), spacer enzymes that use a pair of nucleosomes as their substrate can shift the nucleosome array away from the TSS. Competition between these enzymes results in two types of nucleosome density profiles with well- and ill-positioned +1 nucleosome. Finally, we showed that Pol II assisted histone exchange, if occurring at a fast speed, can abolish the impact of remodeling enzymes. By elucidating the role of individual factors, our study reconciles the seemingly conflicting results on the overall impact of transcription in positioning nucleosomes across species. Nucleosome positioning plays a key role in the genome’s function by regulating the accessibility of protein binding sites as well as higher-order chromatin organization. Though significant progress has been made towards studying the role of DNA sequence in positioning the nucleosomes, our understanding on the impact of transcription lags behind. Our study uses kinetic simulations to explore the role of DNA sequence specificity, transcription factor binding, enzyme remodeling, and Pol II elongation in positioning nucleosomes. It suggests that the differences in nucleosome density profiles observed at various transcription levels in yeast and mouse embryonic stem cells can be understood from a tug-of-war between two types of remodeling enzymes.
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Affiliation(s)
- Zhongling Jiang
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Bin Zhang
- Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- * E-mail:
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17
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Sun L, Pierrakeas L, Li T, Luk E. Thermosensitive Nucleosome Editing Reveals the Role of DNA Sequence in Targeted Histone Variant Deposition. Cell Rep 2021; 30:257-268.e5. [PMID: 31914392 DOI: 10.1016/j.celrep.2019.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 11/04/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022] Open
Abstract
In preparation for transcription, the chromatin remodeler SWR installs homotypic ZZ nucleosomes at promoters by replacing the two nucleosomal H2A with H2A.Z in a stepwise manner. Nucleosome-free regions (NFRs) help recruit SWR to promoters; this is thought to position SWR asymmetrically on one side of the +1 nucleosome. How SWR accesses the opposite side of +1 to generate a ZZ nucleosome remains unclear. Using biochemical assays that monitor the sub-nucleosomal position of nascent H2A.Z, we find that NFR-recruited SWR switches sides to insert H2A.Z into asymmetrically positioned nucleosomes; however, at decreasing temperatures, H2A.Z insertion becomes progressively biased for one side. We find that a 16-bp element containing G/C runs (>3 consecutive G or C nucleotides) is sufficient to promote H2A.Z insertion. Because H2A.Z-rich +1 nucleosomes in yeast have more G/C runs, we propose that nucleosome editing is a thermosensitive process that can be hard coded by the genome.
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Affiliation(s)
- Lu Sun
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Leonidas Pierrakeas
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Tailai Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ed Luk
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA; Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
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18
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Abstract
As primary carriers of epigenetic information and gatekeepers of genomic DNA, nucleosomes are essential for proper growth and development of all eukaryotic cells. Although they are intrinsically dynamic, nucleosomes are actively reorganized by ATP-dependent chromatin remodelers. Chromatin remodelers contain helicase-like ATPase motor domains that can translocate along DNA, and a long-standing question in the field is how this activity is used to reposition or slide nucleosomes. In addition to ratcheting along DNA like their helicase ancestors, remodeler ATPases appear to dictate specific alternating geometries of the DNA duplex, providing an unexpected means for moving DNA past the histone core. Emerging evidence supports twist-based mechanisms for ATP-driven repositioning of nucleosomes along DNA. In this review, we discuss core experimental findings and ideas that have shaped the view of how nucleosome sliding may be achieved.
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Affiliation(s)
- Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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19
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Lehmann LC, Bacic L, Hewitt G, Brackmann K, Sabantsev A, Gaullier G, Pytharopoulou S, Degliesposti G, Okkenhaug H, Tan S, Costa A, Skehel JM, Boulton SJ, Deindl S. Mechanistic Insights into Regulation of the ALC1 Remodeler by the Nucleosome Acidic Patch. Cell Rep 2020; 33:108529. [PMID: 33357431 PMCID: PMC7116876 DOI: 10.1016/j.celrep.2020.108529] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/08/2020] [Accepted: 11/24/2020] [Indexed: 01/09/2023] Open
Abstract
Upon DNA damage, the ALC1/CHD1L nucleosome remodeling enzyme (remodeler) is activated by binding to poly(ADP-ribose). How activated ALC1 recognizes the nucleosome, as well as how this recognition is coupled to remodeling, is unknown. Here, we show that remodeling by ALC1 requires a wild-type acidic patch on the entry side of the nucleosome. The cryo-electron microscopy structure of a nucleosome-ALC1 linker complex reveals a regulatory linker segment that binds to the acidic patch. Mutations within this interface alter the dynamics of ALC1 recruitment to DNA damage and impede the ATPase and remodeling activities of ALC1. Full activation requires acidic patch-linker segment interactions that tether the remodeler to the nucleosome and couple ATP hydrolysis to nucleosome mobilization. Upon DNA damage, such a requirement may be used to modulate ALC1 activity via changes in the nucleosome acidic patches.
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Affiliation(s)
- Laura C Lehmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Klaus Brackmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Guillaume Gaullier
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Sofia Pytharopoulou
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Gianluca Degliesposti
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | | | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.
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20
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Kirk J, Lee JY, Lee Y, Kang C, Shin S, Lee E, Song JJ, Hohng S. Yeast Chd1p Unwraps the Exit Side DNA upon ATP Binding to Facilitate the Nucleosome Translocation Occurring upon ATP Hydrolysis. Biochemistry 2020; 59:4481-4487. [PMID: 33174727 DOI: 10.1021/acs.biochem.0c00747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chromodomain-helicase-DNA-binding protein 1 (CHD1) remodels chromatin by translocating nucleosomes along DNA, but its mechanism remains poorly understood. We use single-molecule fluorescence experiments to clarify the mechanism by which yeast CHD1 (Chd1p) remodels nucleosomes. We find that binding of ATP to Chd1p induces transient unwrapping of the DNA on the exit side of the nucleosome, facilitating nucleosome translocation. ATP hydrolysis is required to induce nucleosome translocation. The unwrapped DNA after translocation is then rewrapped after the release of the hydrolyzed nucleotide and phosphate, revealing that each step of the ATP hydrolysis cycle is responsible for a distinct step of nucleosome remodeling. These results show that Chd1p remodels nucleosomes via a mechanism that is unique among the other ATP-dependent chromatin remodelers.
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Affiliation(s)
- Jaewon Kirk
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
| | - Ju Yeon Lee
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
| | - Yejin Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Chanshin Kang
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
| | - Soochul Shin
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunhye Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
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21
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Bacic L, Sabantsev A, Deindl S. Recent advances in single-molecule fluorescence microscopy render structural biology dynamic. Curr Opin Struct Biol 2020; 65:61-68. [PMID: 32634693 DOI: 10.1016/j.sbi.2020.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 01/30/2023]
Abstract
Single-molecule fluorescence microscopy has long been appreciated as a powerful tool to study the structural dynamics that enable biological function of macromolecules. Recent years have witnessed the development of more complex single-molecule fluorescence techniques as well as powerful combinations with structural approaches to obtain mechanistic insights into the workings of various molecular machines and protein complexes. In this review, we highlight these developments that together bring us one step closer to a dynamic understanding of biological processes in atomic details.
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Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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22
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Sundaram R, Vasudevan D. Structural Basis of Nucleosome Recognition and Modulation. Bioessays 2020; 42:e1900234. [DOI: 10.1002/bies.201900234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 05/05/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Rajivgandhi Sundaram
- Laboratory of Macromolecular Crystallography Institute of Life Sciences Bhubaneswar 751023 India
- Manipal Academy of Higher Education Manipal 576104 India
| | - Dileep Vasudevan
- Laboratory of Macromolecular Crystallography Institute of Life Sciences Bhubaneswar 751023 India
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23
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Singh RK, Fan J, Gioacchini N, Watanabe S, Bilsel O, Peterson CL. Transient Kinetic Analysis of SWR1C-Catalyzed H2A.Z Deposition Unravels the Impact of Nucleosome Dynamics and the Asymmetry of Histone Exchange. Cell Rep 2020; 27:374-386.e4. [PMID: 30970243 PMCID: PMC6545893 DOI: 10.1016/j.celrep.2019.03.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 01/20/2019] [Accepted: 03/08/2019] [Indexed: 12/16/2022] Open
Abstract
The SWR1C chromatin remodeling enzyme catalyzes ATP-dependent replacement of nucleosomal H2A with the H2A.Z variant, regulating key DNA-mediated processes such as transcription and DNA repair. Here, we investigate the transient kinetic mechanism of the histone exchange reaction, employing ensemble FRET, fluorescence correlation spectroscopy (FCS), and the steady-state kinetics of ATP hydrolysis. Our studies indicate that SWR1C modulates nucleosome dynamics on both the millisecond and microsecond timescales, poising the nucleosome for the dimer exchange reaction. The transient kinetic analysis of the remodeling reaction performed under single turnover conditions unraveled a striking asymmetry in the ATP-dependent replacement of nucleosomal dimers, promoted by localized DNA unwrapping. Taken together, our transient kinetic studies identify intermediates and provide crucial insights into the SWR1C-catalyzed dimer exchange reaction and shed light on how the mechanics of H2A.Z deposition might contribute to transcriptional regulation in vivo. The SWR1C remodeling enzyme catalyzes ATP-dependent replacement of nucleosomal H2A with the H2A.Z variant at promoter-proximal nucleosomes. Singh et al. investigate the transient kinetic mechanism of this histone exchange reaction and show that SWR1C transiently unwraps nucleosomal DNA, promoting a concerted dimer eviction and replacement reaction.
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Affiliation(s)
- Raushan K Singh
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jiayl Fan
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan Gioacchini
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shinya Watanabe
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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24
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Zhong Y, Paudel BP, Ryan DP, Low JKK, Franck C, Patel K, Bedward MJ, Torrado M, Payne RJ, van Oijen AM, Mackay JP. CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation. Nat Commun 2020; 11:1519. [PMID: 32251276 PMCID: PMC7090039 DOI: 10.1038/s41467-020-15183-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 02/21/2020] [Indexed: 11/09/2022] Open
Abstract
Chromatin remodellers hydrolyse ATP to move nucleosomal DNA against histone octamers. The mechanism, however, is only partially resolved, and it is unclear if it is conserved among the four remodeller families. Here we use single-molecule assays to examine the mechanism of action of CHD4, which is part of the least well understood family. We demonstrate that the binding energy for CHD4-nucleosome complex formation-even in the absence of nucleotide-triggers significant conformational changes in DNA at the entry side, effectively priming the system for remodelling. During remodelling, flanking DNA enters the nucleosome in a continuous, gradual manner but exits in concerted 4-6 base-pair steps. This decoupling of entry- and exit-side translocation suggests that ATP-driven movement of entry-side DNA builds up strain inside the nucleosome that is subsequently released at the exit side by DNA expulsion. Based on our work and previous studies, we propose a mechanism for nucleosome sliding.
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Affiliation(s)
- Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Bishnu P Paudel
- Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Daniel P Ryan
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Charlotte Franck
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Max J Bedward
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Antoine M van Oijen
- Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia. .,Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
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25
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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26
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Yan L, Chen Z. A Unifying Mechanism of DNA Translocation Underlying Chromatin Remodeling. Trends Biochem Sci 2019; 45:217-227. [PMID: 31623923 DOI: 10.1016/j.tibs.2019.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 12/18/2022]
Abstract
Chromatin remodelers alter the position and composition of nucleosomes, and play key roles in the regulation of chromatin structure and various chromatin-based transactions. Recent cryo-electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) studies have shed mechanistic light on the fundamental question of how the remodeling enzymes couple with ATP hydrolysis to slide nucleosomes. Structures of the chromatin remodeler Snf2 bound to the nucleosome reveal the conformational cycle of the enzyme and the induced DNA distortion. Investigations on ISWI, Chd1, and INO80 support a unifying fundamental mechanism of DNA translocation. Finally, studies of the SWR1 complex suggest that the enzyme distorts the DNA abnormally to achieve histone exchange without net DNA translocation.
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Affiliation(s)
- Lijuan Yan
- Ministry of Education (MOE) Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, PRC; School of Life Science, Tsinghua University, Beijing 100084, PRC
| | - Zhucheng Chen
- Ministry of Education (MOE) Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, PRC; School of Life Science, Tsinghua University, Beijing 100084, PRC; Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing 100084, PRC.
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27
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Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD. The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res 2019; 46:4978-4990. [PMID: 29850894 PMCID: PMC6007315 DOI: 10.1093/nar/gky206] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/16/2018] [Indexed: 01/21/2023] Open
Abstract
Chromatin remodelers are ATP-dependent motors that reorganize DNA packaging by disrupting canonical histone–DNA contacts within the nucleosome. Here, we show that the Chd1 chromatin remodeler stimulates DNA unwrapping from the edge of the nucleosome in a nucleotide-dependent and DNA sequence-sensitive fashion. Nucleosome binding, monitored by stopped flow, was complex and sensitive to nucleotide, with AMP–PNP promoting faster binding than ADP·BeF3–. Nucleosome unwrapping by Chd1, examined by bulk FRET, occurred in the presence and absence of nucleotide and did not require the Chd1 DNA-binding domain. In AMP–PNP conditions, Chd1 unwrapped one side of the Widom 601 DNA more easily than the other, consistent with previous observations of 601 asymmetry and indicating that Chd1 amplifies intrinsic sequence properties of nucleosomal DNA. Using small angle X-ray scattering (SAXS) with contrast variation, we found distinct DNA conformations depending on the nucleotide analog bound to Chd1: with AMP–PNP, DNA primarily unwrapped in-plane with the nucleosomal disk, whereas with ADP·BeF3–, a significant fraction showed distinctive out-of-plane unwrapping as well. Taken together, our findings show tight coupling between entry/exit DNA of the nucleosome and the Chd1 ATPase motor, suggesting that dynamic nucleosome unwrapping is coupled to nucleosome binding and remodeling by Chd1.
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Affiliation(s)
- Joshua M Tokuda
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Ren Ren
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Rebecca J Tay
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Ming Yan
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
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28
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Affiliation(s)
- Michaela M Smolle
- Biomedical Center, Faculty of Medicine, Ludwig-Maximilians University of Munich, Martinsried-Planegg, Germany.
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29
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Wild P, Susperregui A, Piazza I, Dörig C, Oke A, Arter M, Yamaguchi M, Hilditch AT, Vuina K, Chan KC, Gromova T, Haber JE, Fung JC, Picotti P, Matos J. Network Rewiring of Homologous Recombination Enzymes during Mitotic Proliferation and Meiosis. Mol Cell 2019; 75:859-874.e4. [PMID: 31351878 PMCID: PMC6715774 DOI: 10.1016/j.molcel.2019.06.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/24/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023]
Abstract
Homologous recombination (HR) is essential for high-fidelity DNA repair during mitotic proliferation and meiosis. Yet, context-specific modifications must tailor the recombination machinery to avoid (mitosis) or enforce (meiosis) the formation of reciprocal exchanges-crossovers-between recombining chromosomes. To obtain molecular insight into how crossover control is achieved, we affinity purified 7 DNA-processing enzymes that channel HR intermediates into crossovers or noncrossovers from vegetative cells or cells undergoing meiosis. Using mass spectrometry, we provide a global characterization of their composition and reveal mitosis- and meiosis-specific modules in the interaction networks. Functional analyses of meiosis-specific interactors of MutLγ-Exo1 identified Rtk1, Caf120, and Chd1 as regulators of crossing-over. Chd1, which transiently associates with Exo1 at the prophase-to-metaphase I transition, enables the formation of MutLγ-dependent crossovers through its conserved ability to bind and displace nucleosomes. Thus, rewiring of the HR network, coupled to chromatin remodeling, promotes context-specific control of the recombination outcome.
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Affiliation(s)
- Philipp Wild
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Aitor Susperregui
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ilaria Piazza
- Institute of Molecular Systems Biology, HPM-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Christian Dörig
- Institute of Molecular Systems Biology, HPM-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ashwini Oke
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Meret Arter
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Miyuki Yamaguchi
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | - Alexander T Hilditch
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Karla Vuina
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ki Choi Chan
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Tatiana Gromova
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | - Jennifer C Fung
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Paola Picotti
- Institute of Molecular Systems Biology, HPM-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Joao Matos
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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30
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Armache JP, Gamarra N, Johnson SL, Leonard JD, Wu S, Narlikar GJ, Cheng Y. Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. eLife 2019; 8:46057. [PMID: 31210637 PMCID: PMC6611695 DOI: 10.7554/elife.46057] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/18/2019] [Indexed: 12/24/2022] Open
Abstract
The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture two potential reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn't show octamer deformation, but surprisingly shows a 2 bp translocation. FRET studies indicate that ADP-BeFx predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation.
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Affiliation(s)
- Jean Paul Armache
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - 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
| | - Stephanie L Johnson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - John D Leonard
- 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
| | - Shenping Wu
- Howard Hughes Medical Institute, 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
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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31
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Levendosky RF, Bowman GD. Asymmetry between the two acidic patches dictates the direction of nucleosome sliding by the ISWI chromatin remodeler. eLife 2019; 8:45472. [PMID: 31094676 PMCID: PMC6546392 DOI: 10.7554/elife.45472] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/16/2019] [Indexed: 01/15/2023] Open
Abstract
The acidic patch is a functionally important epitope on each face of the nucleosome that affects chromatin remodeling. Although related by 2-fold symmetry of the nucleosome, each acidic patch is uniquely positioned relative to a bound remodeler. An open question is whether remodelers are distinctly responsive to each acidic patch. Previously we reported a method for homogeneously producing asymmetric nucleosomes with distinct H2A/H2B dimers (Levendosky et al., 2016). Here, we use this methodology to show that the Chd1 remodeler from Saccharomyces cerevisiae and ISWI remodelers from human and Drosophila have distinct spatial requirements for the acidic patch. Unlike Chd1, which is equally affected by entry- and exit-side mutations, ISWI remodelers strongly depend on the entry-side acidic patch. Remarkably, asymmetry in the two acidic patches stimulates ISWI to slide mononucleosomes off DNA ends, overriding the remodeler’s preference to shift the histone core toward longer flanking DNA.
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Affiliation(s)
- Robert F Levendosky
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Gregory D Bowman
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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32
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Tippana R, Chen MC, Demeshkina NA, Ferré-D'Amaré AR, Myong S. RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36. Nat Commun 2019; 10:1855. [PMID: 31015431 PMCID: PMC6478676 DOI: 10.1038/s41467-019-09802-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
DHX36 is a DEAH-box helicase that resolves parallel G-quadruplex structures formed in DNA and RNA. The recent co-crystal structure of DHX36 bound G4-DNA revealed an intimate contact, but did not address the role of ATP hydrolysis in G4 resolving activity. Here, we demonstrate that unlike on G4-DNA, DHX36 displays ATP-independent unfolding of G4-RNA followed by ATP-dependent refolding, generating a highly asymmetric pattern of activity. Interestingly, DHX36 refolds G4-RNA in several steps, reflecting the discrete steps in forming the G4 structure. We show that the ATP-dependent activity of DHX36 arises from the RNA tail rather than the G4. Mutations that perturb G4 contact result in quick dissociation of the protein from RNA upon ATP hydrolysis, while mutations that interfere with binding the RNA tail induce dysregulated activity. We propose that the ATP-dependent activity of DHX36 may be useful for dynamically resolving various G4-RNA structures in cells.
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Affiliation(s)
- Ramreddy Tippana
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Michael C Chen
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1TN, UK.,Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Natalia A Demeshkina
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL, 61801, USA.
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33
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Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling. Nat Commun 2019; 10:1720. [PMID: 30979890 PMCID: PMC6461674 DOI: 10.1038/s41467-019-09657-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/20/2019] [Indexed: 11/11/2022] Open
Abstract
ATP-dependent chromatin remodelling enzymes (remodellers) regulate DNA accessibility in eukaryotic genomes. Many remodellers reposition (slide) nucleosomes, however, how DNA is propagated around the histone octamer during this process is unclear. Here we examine the real-time coordination of remodeller-induced DNA movements on both sides of the nucleosome using three-colour single-molecule FRET. During sliding by Chd1 and SNF2h remodellers, DNA is shifted discontinuously, with movement of entry-side DNA preceding that of exit-side DNA. The temporal delay between these movements implies a single rate-limiting step dependent on ATP binding and transient absorption or buffering of at least one base pair. High-resolution cross-linking experiments show that sliding can be achieved by buffering as few as 3 bp between entry and exit sides of the nucleosome. We propose that DNA buffering ensures nucleosome stability during ATP-dependent remodelling, and provides a means for communication between remodellers acting on opposite sides of the nucleosome. Chromatin remodelling enzymes (remodellers) regulate DNA accessibility of eukaryotic genomes, which rely in large part on an ability to reposition nucleosomes. Here the authors use three-colour single-molecule FRET to simultaneously monitor remodeller-induced DNA movements on both sides of the nucleosome in real-time.
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34
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Schoberleitner I, Mutti A, Sah A, Wille A, Gimeno-Valiente F, Piatti P, Kharitonova M, Torres L, López-Rodas G, Liu JJ, Singewald N, Schwarzer C, Lusser A. Role for Chromatin Remodeling Factor Chd1 in Learning and Memory. Front Mol Neurosci 2019; 12:3. [PMID: 30728766 PMCID: PMC6351481 DOI: 10.3389/fnmol.2019.00003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/08/2019] [Indexed: 12/21/2022] Open
Abstract
Precise temporal and spatial regulation of gene expression in the brain is a prerequisite for cognitive processes such as learning and memory. Epigenetic mechanisms that modulate the chromatin structure have emerged as important regulators in this context. While posttranslational modification of histones or the modification of DNA bases have been examined in detail in many studies, the role of ATP-dependent chromatin remodeling factors (ChRFs) in learning- and memory-associated gene regulation has largely remained obscure. Here we present data that implicate the highly conserved chromatin assembly and remodeling factor Chd1 in memory formation and the control of immediate early gene (IEG) response in the hippocampus. We used various paradigms to assess short-and long-term memory in mice bearing a mutated Chd1 gene that gives rise to an N-terminally truncated protein. Our data demonstrate that the Chd1 mutation negatively affects long-term object recognition and short- and long-term spatial memory. We found that Chd1 regulates hippocampal expression of the IEG early growth response 1 (Egr1) and activity-regulated cytoskeleton-associated (Arc) but not cFos and brain derived neurotrophic factor (Bdnf), because the Chd1-mutation led to dysregulation of Egr1 and Arc expression in naive mice and in mice analyzed at different stages of object location memory (OLM) testing. Of note, Chd1 likely regulates Egr1 in a direct manner, because chromatin immunoprecipitation (ChIP) assays revealed enrichment of Chd1 upon stimulation at the Egr1 genomic locus in the hippocampus and in cultured cells. Together these data support a role for Chd1 as a critical regulator of molecular mechanisms governing memory-related processes, and they show that this function involves the N-terminal serine-rich region of the protein.
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Affiliation(s)
- Ines Schoberleitner
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna Mutti
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Anupam Sah
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Centre for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Alexandra Wille
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Francisco Gimeno-Valiente
- Institute of Health Research, INCLIVA, and Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Paolo Piatti
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Maria Kharitonova
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Centre for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Luis Torres
- Institute of Health Research, INCLIVA, and Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Gerardo López-Rodas
- Institute of Health Research, INCLIVA, and Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Jeffrey J. Liu
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Centre for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Christoph Schwarzer
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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35
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Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T. Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. eLife 2018; 7:35720. [PMID: 30079888 PMCID: PMC6118821 DOI: 10.7554/elife.35720] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/24/2018] [Indexed: 12/23/2022] Open
Abstract
ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.
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Affiliation(s)
| | - Amanda L Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hassane El-Mkami
- School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
| | - David G Norman
- Nucleic Acids Structure Research Group, University of Dundee, Dundee, United Kingdom
| | - Helder Ferreira
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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36
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Kim H, Jo H, Seo HD, Park HS, Lee D. Chd1p recognizes H3K36Ac to maintain nucleosome positioning near the transcription start site. Biochem Biophys Res Commun 2018; 503:1200-1206. [PMID: 30005873 DOI: 10.1016/j.bbrc.2018.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
In Saccharomyces cerevisiae, the ATP-dependent chromatin remodeler, Chd1p, globally affects nucleosome positioning at coding regions, where nucleosomes are specifically and directionally aligned with respect to the transcription start site (TSS). Various auxiliary domains of remodelers play critical roles by performing specialized functions that are unique to the type of remodeler. Here, we report that yeast Chd1p directly binds to acetylated histone H3K36 (H3K36Ac) via its chromodomain, and that H3K36Ac stimulates the nucleosome sliding activity of Chd1p in vitro. Furthermore, we use genome-wide analysis to demonstrate that H3K36Ac promotes the remodeling activity of Chd1p to maintain chromatin stability at the 5' ends of genes in vivo. Our work linking Chd1p with H3K36Ac provides novel insights into how the nucleosome remodeling activity of Chd1p is controlled near the TSS.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea
| | - Hyelim Jo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea
| | - Hogyu David Seo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea.
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37
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Ayala R, Willhoft O, Aramayo RJ, Wilkinson M, McCormack EA, Ocloo L, Wigley DB, Zhang X. Structure and regulation of the human INO80-nucleosome complex. Nature 2018; 556:391-395. [PMID: 29643506 PMCID: PMC5937682 DOI: 10.1038/s41586-018-0021-6] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/16/2018] [Indexed: 01/15/2023]
Abstract
Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines 1 . Biochemical studies2-4 have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2-a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)-in complex with nucleosomes5-7 have provided insights into the basic mechanism of nucleosome sliding performed by these complexes. However, how larger, multi-subunit remodelling complexes such as INO80 interact with nucleosomes and how remodellers carry out functions such as nucleosome sliding 8 , histone exchange 9 and nucleosome spacing10-12 remain poorly understood. Although some remodellers work as monomers 13 , others work as highly cooperative dimers11, 14, 15. Here we present the structure of the human INO80 chromatin remodeller with a bound nucleosome, which reveals that INO80 interacts with nucleosomes in a previously undescribed manner: the motor domains are located on the DNA at the entry point to the nucleosome, rather than at superhelical location 2. The ARP5-IES6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This arrangement enables the histone H3 tails of the nucleosome to have a role in the regulation of the activities of the INO80 motor domain-unlike in other characterized remodellers, for which H4 tails have been shown to regulate the motor domains.
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Affiliation(s)
- Rafael Ayala
- Section of Structural Biology, Dept. Medicine, Imperial College London, London, UK
| | - Oliver Willhoft
- Section of Structural Biology, Dept. Medicine, Imperial College London, London, UK
| | - Ricardo J Aramayo
- Section of Structural Biology, Dept. Medicine, Imperial College London, London, UK
| | - Martin Wilkinson
- Section of Structural Biology, Dept. Medicine, Imperial College London, London, UK
| | | | - Lorraine Ocloo
- Section of Structural Biology, Dept. Medicine, Imperial College London, London, UK
| | - Dale B Wigley
- Section of Structural Biology, Dept. Medicine, Imperial College London, London, UK.
| | - Xiaodong Zhang
- Section of Structural Biology, Dept. Medicine, Imperial College London, London, UK.
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38
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Qiu Y, Koh HR, Myong S. Probing Dynamic Assembly and Disassembly of Rad51 Tuned by Srs2 Using smFRET. Methods Enzymol 2018; 600:321-345. [PMID: 29458765 DOI: 10.1016/bs.mie.2018.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The integrity of DNA is critical for sustaining the life of any living organism, as DNA is a reservoir of its genetic information. However, DNA is continuously damaged by either normal metabolic pathways or environmental insults such as ultraviolet exposure or chemicals. Double-stranded DNA break is one of the most common types of DNA damage that requires activation of homologous recombination (HR) pathway mediated by Rad51 in eukaryotes (Paques & Haber, 1999; Symington, 2002). Rad51 protein forms a helical nucleoprotein filament on resected DNA to initiate homology search but also can interact with other single-stranded DNA (ssDNA)-binding proteins including Srs2. Srs2, a well-known antirecombinase in HR, is an ATP-dependent 3'-5' DNA helicase in the budding yeast Saccharomyces cerevisiae as well as an ssDNA translocase. It disrupts Rad51 filaments, preventing HR (Krejci et al., 2003; Le Breton et al., 2008; Veaute et al., 2003). In the following text, we provide detailed experimental platforms employed to investigate the activity of Rad51 and Srs2 using single-molecule Forster resonance energy transfer and protein-induced fluorescence enhancement. First, we demonstrate how to detect Rad51 filament formation to address the binding site size binding kinetic of the Rad51, as well as the directionality of the filament formation. Next, we explain how to visualize ATP-dependent translocation and unwinding activities of Srs2 on DNA. Lastly, we demonstrate the filament forming activity by Rad51 which is counteracted by the filament removal activity of Srs2.
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Affiliation(s)
- Yupeng Qiu
- Johns Hopkins University, Baltimore, MD, United States
| | - Hye Ran Koh
- Johns Hopkins University, Baltimore, MD, United States; Chung-Ang University, Seoul, South Korea
| | - Sua Myong
- Johns Hopkins University, Baltimore, MD, United States.
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39
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Schwarz M, Schall K, Kallis E, Eustermann S, Guariento M, Moldt M, Hopfner KP, Michaelis J. Single-molecule nucleosome remodeling by INO80 and effects of histone tails. FEBS Lett 2018; 592:318-331. [PMID: 29331030 DOI: 10.1002/1873-3468.12973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/22/2017] [Accepted: 12/29/2017] [Indexed: 01/30/2023]
Abstract
Genome maintenance and integrity requires continuous alterations of the compaction state of the chromatin structure. Chromatin remodelers, among others the INO80 complex, help organize chromatin by repositioning, reshaping, or evicting nucleosomes. We report on INO80 nucleosome remodeling, assayed by single-molecule Foerster resonance energy transfer on canonical nucleosomes as well as nucleosomes assembled from tailless histones. Nucleosome repositioning by INO80 is a processively catalyzed reaction. During the initiation of remodeling, probed by the INO80 bound state, the nucleosome reveals structurally heterogeneous states for tailless nucleosomes (in contrast to wild-type nucleosomes). We, therefore, propose an altered energy landscape for the INO80-mediated nucleosome sliding reaction in the absence of histone tails.
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Affiliation(s)
- Marianne Schwarz
- Faculty of Natural Sciences, Institute of Biophysics, Ulm University, Germany.,Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kevin Schall
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Eleni Kallis
- Faculty of Natural Sciences, Institute of Biophysics, Ulm University, Germany
| | - Sebastian Eustermann
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Mara Guariento
- Faculty of Natural Sciences, Institute of Biophysics, Ulm University, Germany
| | - Manuela Moldt
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Jens Michaelis
- Faculty of Natural Sciences, Institute of Biophysics, Ulm University, Germany
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