1
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Guzmán-Dinamarca B, Conejeros R, Rivas-Astroza M. Dynamic metabolic regulation of histone modifications during the yeast metabolic cycle. PLoS One 2025; 20:e0323242. [PMID: 40392806 PMCID: PMC12091797 DOI: 10.1371/journal.pone.0323242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2024] [Accepted: 04/04/2025] [Indexed: 05/22/2025] Open
Abstract
Eukaryotes achieve a wide range of stable phenotypes by virtue of epigenetic modifications. However, what drives epigenetic diversification in the first place remains an open question. Here, we investigated the dynamic interplay between the production fluxes of epigenetic cosubstrates and histone post-translation modifications (PTMs) in Saccharomyces cerevisiae's Yeast Metabolic Cycle (YMC). We developed a novel approach integrating flux analysis with transcriptomic data to investigate the production fluxes of acetyl-CoA and SAM and their influence on histone marks H3K9Ac and H3K4me3. Our results show that acetyl-CoA and SAM flux dynamics are asynchronous during the YMC, suggesting distinct regulatory roles. Gene ontology analysis revealed that genes whose enrichment of H3K9Ac correlates with acetyl-CoA dynamics are associated with metabolic functions, while genes whose enrichment of H3K4me3 correlates with SAM dynamics are associated with translation processes. Finally, we found evidence that chromatin accessibility on genes promoter regions was a precondition for the metabolic fluxes influencing the enrichment of H3K4me3 and H3K9Ac. These findings support the concept that metabolism provides timely cosubstrates essential for histone PTMs.
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Affiliation(s)
| | - Raúl Conejeros
- Pontificia Universidad Católica de Valparaíso, Escuela de Ingeniería Bioquímica, Valparaíso, Chile
| | - Marcelo Rivas-Astroza
- Universidad Tecnológica Metropolitana, Departamento de Biotecnología, Santiago, Chile
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2
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James AM, Farnung L. Structural basis of human CHD1 nucleosome recruitment and pausing. Mol Cell 2025; 85:1938-1951.e6. [PMID: 40334658 DOI: 10.1016/j.molcel.2025.04.020] [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] [Received: 11/14/2024] [Revised: 02/26/2025] [Accepted: 04/16/2025] [Indexed: 05/09/2025]
Abstract
Chromatin remodelers regulate gene expression and genome maintenance by controlling nucleosome positioning, but the structural basis for their regulated and directional activity remains poorly understood. Here, we present three cryoelectron microscopy (cryo-EM) structures of human chromodomain helicase DNA-binding protein 1 (CHD1) bound to nucleosomes that reveal previously unobserved recruitment and regulatory states. We identify a structural element, termed the "anchor element," that connects the CHD1 ATPase motor to the nucleosome entry-side acidic patch. The anchor element coordinates with other regulatory modules, including the gating element, which undergoes a conformational switch critical for remodeling. Our structures demonstrate how the DNA-binding region of CHD1 binds entry- and exit-side DNA during remodeling to achieve directional sliding. The observed structural elements are conserved across chromatin remodelers, suggesting a unified mechanism for nucleosome recognition and remodeling. Our findings show how chromatin remodelers couple nucleosome recruitment to regulated DNA translocation, providing a framework for understanding chromatin remodeler mechanisms beyond DNA translocation.
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Affiliation(s)
- Allison M James
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lucas Farnung
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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3
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Farnung L. Nucleosomes unwrapped: Structural perspectives on transcription through chromatin. Curr Opin Struct Biol 2023; 82:102690. [PMID: 37633188 DOI: 10.1016/j.sbi.2023.102690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Transcription of most protein-coding genes requires the passage of RNA polymerase II through chromatin. Chromatin with its fundamental unit, the nucleosome, represents a barrier to transcription. How RNA polymerase II and associated factors traverse through nucleosomes and how chromatin architecture is maintained have remained largely enigmatic. Only recently, cryo-EM structures have visualized the transcription process through chromatin. These structures have elucidated how transcription initiation and transcription elongation influence and are influenced by a chromatinized DNA substrate. This review provides a summary of our current structural understanding of transcription through chromatin, highlighting common mechanisms during nucleosomal traversal and novel regulatory mechanisms that have emerged in the last five years.
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Affiliation(s)
- Lucas Farnung
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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4
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Tan ZY, Cai S, Noble AJ, Chen JK, Shi J, Gan L. Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ. eLife 2023; 12:RP87672. [PMID: 37503920 PMCID: PMC10382156 DOI: 10.7554/elife.87672] [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] [Indexed: 07/29/2023] Open
Abstract
Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ is otherwise poorly understood. Using cryo-electron tomography (cryo-ET) and 3D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expected in situ. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are found ex vivo (in nuclear lysates), but not in situ. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosome's DNA is partially detached in situ.
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Affiliation(s)
- Zhi Yang Tan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Shujun Cai
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Jon K Chen
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Jian Shi
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Lu Gan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
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5
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Sabantsev A, Mao G, Aguirre Rivera J, Panfilov M, Arseniev A, Ho O, Khodorkovskiy M, Deindl S. Spatiotemporally controlled generation of NTPs for single-molecule studies. Nat Chem Biol 2022; 18:1144-1151. [PMID: 36131148 PMCID: PMC9512701 DOI: 10.1038/s41589-022-01100-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/29/2022] [Indexed: 12/22/2022]
Abstract
Many essential processes in the cell depend on proteins that use nucleoside triphosphates (NTPs). Methods that directly monitor the often-complex dynamics of these proteins at the single-molecule level have helped to uncover their mechanisms of action. However, the measurement throughput is typically limited for NTP-utilizing reactions, and the quantitative dissection of complex dynamics over multiple sequential turnovers remains challenging. Here we present a method for controlling NTP-driven reactions in single-molecule experiments via the local generation of NTPs (LAGOON) that markedly increases the measurement throughput and enables single-turnover observations. We demonstrate the effectiveness of LAGOON in single-molecule fluorescence and force spectroscopy assays by monitoring DNA unwinding, nucleosome sliding and RNA polymerase elongation. LAGOON can be readily integrated with many single-molecule techniques, and we anticipate that it will facilitate studies of a wide range of crucial NTP-driven processes.
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Affiliation(s)
- Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Javier Aguirre Rivera
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mikhail Panfilov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Anatolii Arseniev
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Oanh Ho
- 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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6
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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7
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Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S. Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome. eLife 2021; 10:e71420. [PMID: 34486521 PMCID: PMC8463071 DOI: 10.7554/elife.71420] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/05/2021] [Indexed: 12/21/2022] Open
Abstract
The chromatin remodeler ALC1 is recruited to and activated by DNA damage-induced poly(ADP-ribose) (PAR) chains deposited by PARP1/PARP2/HPF1 upon detection of DNA lesions. ALC1 has emerged as a candidate drug target for cancer therapy as its loss confers synthetic lethality in homologous recombination-deficient cells. However, structure-based drug design and molecular analysis of ALC1 have been hindered by the requirement for PARylation and the highly heterogeneous nature of this post-translational modification. Here, we reconstituted an ALC1 and PARylated nucleosome complex modified in vitro using PARP2 and HPF1. This complex was amenable to cryo-EM structure determination without cross-linking, which enabled visualization of several intermediate states of ALC1 from the recognition of the PARylated nucleosome to the tight binding and activation of the remodeler. Functional biochemical assays with PARylated nucleosomes highlight the importance of nucleosomal epitopes for productive remodeling and suggest that ALC1 preferentially slides nucleosomes away from DNA breaks.
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Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Guillaume Gaullier
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Laura C Lehmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Klaus Brackmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Despoina Dimakou
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Mario Halic
- Department of Structural Biology, St Jude Children's Research HospitalMemphisUnited States
| | | | | | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
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8
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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9
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Hoffmeister H, Fuchs A, Komives E, Groebner-Ferreira R, Strobl L, Nazet J, Heizinger L, Merkl R, Dove S, Längst G. Sequence and functional differences in the ATPase domains of CHD3 and SNF2H promise potential for selective regulability and drugability. FEBS J 2021; 288:4000-4023. [PMID: 33403747 DOI: 10.1111/febs.15699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/19/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022]
Abstract
Chromatin remodelers use the energy of ATP hydrolysis to regulate chromatin dynamics. Their impact for development and disease requires strict enzymatic control. Here, we address the differential regulability of the ATPase domain of hSNF2H and hCHD3, exhibiting similar substrate affinities and enzymatic activities. Both enzymes are comparably strongly inhibited in their ATP hydrolysis activity by the competitive ATPase inhibitor ADP. However, the nucleosome remodeling activity of SNF2H is more strongly affected than that of CHD3. Beside ADP, also IP6 inhibits the nucleosome translocation of both enzymes to varying degrees, following a competitive inhibition mode at CHD3, but not at SNF2H. Our observations are further substantiated by mutating conserved Q- and K-residues of ATPase domain motifs. The variants still bind both substrates and exhibit a wild-type similar, basal ATP hydrolysis. Apart from three CHD3 variants, none of the variants can translocate nucleosomes, suggesting for the first time that the basal ATPase activity of CHD3 is sufficient for nucleosome remodeling. Together with the ADP data, our results propose a more efficient coupling of ATP hydrolysis and remodeling in CHD3. This aspect correlates with findings that CHD3 nucleosome translocation is visible at much lower ATP concentrations than SNF2H. We propose sequence differences between the ATPase domains of both enzymes as an explanation for the functional differences and suggest that aa interactions, including the conserved Q- and K-residues distinctly regulate ATPase-dependent functions of both proteins. Our data emphasize the benefits of remodeler ATPase domains for selective drugability and/or regulability of chromatin dynamics.
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Affiliation(s)
- Helen Hoffmeister
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
| | - Andreas Fuchs
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
| | - Elizabeth Komives
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Regina Groebner-Ferreira
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
| | - Laura Strobl
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
| | - Julian Nazet
- Department of Biochemistry II, University of Regensburg, Germany
| | | | - Rainer Merkl
- Department of Biochemistry II, University of Regensburg, Germany
| | - Stefan Dove
- Department of Pharmaceutical and Medical Chemistry II, University of Regensburg, Germany
| | - Gernot Längst
- Department of Biochemistry, Genetics and Microbiology, Biochemistry III, University of Regensburg, Germany
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10
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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: 0.4] [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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11
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Abstract
ATP-dependent chromatin remodelling enzymes are molecular machines that act to reconfigure the structure of nucleosomes. Until recently, little was known about the structure of these enzymes. Recent progress has revealed that their interaction with chromatin is dominated by ATPase domains that contact DNA at favoured locations on the nucleosome surface. Contacts with histones are limited but play important roles in modulating activity. The ATPase domains do not act in isolation but are flanked by diverse accessory domains and subunits. New structures indicate how these subunits are arranged in multi-subunit complexes providing a framework from which to understand how a common motor is applied to distinct functions.
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Affiliation(s)
- Ramasubramian Sundaramoorthy
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, Dundee, DD1 5EH, UK
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12
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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: 23] [Impact Index Per Article: 4.6] [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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13
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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: 1.4] [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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14
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Farnung L, Ochmann M, Cramer P. Nucleosome-CHD4 chromatin remodeler structure maps human disease mutations. eLife 2020; 9:56178. [PMID: 32543371 PMCID: PMC7338049 DOI: 10.7554/elife.56178] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Chromatin remodeling plays important roles in gene regulation during development, differentiation and in disease. The chromatin remodeling enzyme CHD4 is a component of the NuRD and ChAHP complexes that are involved in gene repression. Here, we report the cryo-electron microscopy (cryo-EM) structure of Homo sapiens CHD4 engaged with a nucleosome core particle in the presence of the non-hydrolysable ATP analogue AMP-PNP at an overall resolution of 3.1 Å. The ATPase motor of CHD4 binds and distorts nucleosomal DNA at superhelical location (SHL) +2, supporting the ‘twist defect’ model of chromatin remodeling. CHD4 does not induce unwrapping of terminal DNA, in contrast to its homologue Chd1, which functions in gene activation. Our structure also maps CHD4 mutations that are associated with human cancer or the intellectual disability disorder Sifrim-Hitz-Weiss syndrome.
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Affiliation(s)
- Lucas Farnung
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Moritz Ochmann
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
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15
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Han Y, Reyes AA, Malik S, He Y. Cryo-EM structure of SWI/SNF complex bound to a nucleosome. Nature 2020; 579:452-455. [PMID: 32188938 PMCID: PMC7319049 DOI: 10.1038/s41586-020-2087-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
The chromatin-remodelling complex SWI/SNF is highly conserved and has critical roles in various cellular processes, including transcription and DNA-damage repair1,2. It hydrolyses ATP to remodel chromatin structure by sliding and evicting histone octamers3-8, creating DNA regions that become accessible to other essential factors. However, our mechanistic understanding of the remodelling activity is hindered by the lack of a high-resolution structure of complexes from this family. Here we report the cryo-electron microscopy structure of Saccharomyces cerevisiae SWI/SNF bound to a nucleosome, at near-atomic resolution. In the structure, the actin-related protein (Arp) module is sandwiched between the ATPase and the rest of the complex, with the Snf2 helicase-SANT associated (HSA) domain connecting all modules. The body contains an assembly scaffold composed of conserved subunits Snf12 (also known as SMARCD or BAF60), Snf5 (also known as SMARCB1, BAF47 or INI1) and an asymmetric dimer of Swi3 (also known as SMARCC, BAF155 or BAF170). Another conserved subunit, Swi1 (also known as ARID1 or BAF250), resides in the core of SWI/SNF, acting as a molecular hub. We also observed interactions between Snf5 and the histones at the acidic patch, which could serve as an anchor during active DNA translocation. Our structure enables us to map and rationalize a subset of cancer-related mutations in the human SWI/SNF complex and to propose a model for how SWI/SNF recognizes and remodels the +1 nucleosome to generate nucleosome-depleted regions during gene activation9.
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Affiliation(s)
- Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Alexis A Reyes
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, USA
| | - Sara Malik
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA. .,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA.
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16
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Blossey R, Schiessel H. Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: Confronting theory and high-throughput experiments. Phys Rev E 2019; 99:060401. [PMID: 31330635 DOI: 10.1103/physreve.99.060401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Indexed: 12/13/2022]
Abstract
Chromatin remodelers are multidomain enzymatic motor complexes that displace nucleosomes along DNA and hence "remodel chromatin structure," i.e., they dynamically reorganize nucleosome positions in both gene activation and gene repression. Recently, experimental insights from structural biology methods and remodeling assays have substantially advanced the understanding of these key chromatin components. Here we confront the kinetic proofreading scenario of chromatin remodeling, which proposes a mechanical link between histone residue modifications and the ATP-dependent action of remodelers, with recent experiments. We show that recent high-throughput data on nucleosome libraries assayed with remodelers from the Imitation Switch family are in accord with our earlier predictions of the kinetic proofreading scenario. We make suggestions for experimentally verifiable predictions of the kinetic proofreading scenarios for remodelers from other families.
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Affiliation(s)
- Ralf Blossey
- Université de Lille, CNRS, UMR8576 Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), F-59000 Lille, France
| | - Helmut Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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17
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Chittori S, Hong J, Bai Y, Subramaniam S. Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome. Nucleic Acids Res 2019; 47:9400-9409. [PMID: 31402386 PMCID: PMC6755096 DOI: 10.1093/nar/gkz670] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/11/2019] [Accepted: 08/03/2019] [Indexed: 12/15/2022] Open
Abstract
ATP-dependent chromatin remodeling factors of SWI/SNF2 family including ISWI, SNF2, CHD1 and INO80 subfamilies share a conserved but functionally non-interchangeable ATPase domain. Here we report cryo-electron microscopy (cryo-EM) structures of the nucleosome bound to an ISWI fragment with deletion of the AutoN and HSS regions in nucleotide-free conditions and the free nucleosome at ∼ 4 Å resolution. In the bound conformation, the ATPase domain interacts with the super helical location 2 (SHL 2) of the nucleosomal DNA, with the N-terminal tail of H4 and with the α1 helix of H3. Density for other regions of ISWI is not observed, presumably due to disorder. Comparison with the structure of the free nucleosome reveals that although the histone core remains largely unchanged, remodeler binding causes perturbations in the nucleosomal DNA resulting in a bulge near the SHL2 site. Overall, the structure of the nucleotide-free ISWI-nucleosome complex is similar to the corresponding regions of the recently reported ADP bound ISWI-nucleosome structures, which are significantly different from that observed for the ADP-BeFx bound structure. Our findings are relevant to the initial step of ISWI binding to the nucleosome and provide additional insights into the nucleosome remodeling process driven by ISWI.
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Affiliation(s)
- Sagar Chittori
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Jingjun Hong
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Sriram Subramaniam
- University of British Columbia, Vancouver, British Columbia, Canada.,Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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18
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Breitgoff FD, Keller K, Qi M, Klose D, Yulikov M, Godt A, Jeschke G. UWB DEER and RIDME distance measurements in Cu(II)-Cu(II) spin pairs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106560. [PMID: 31377151 DOI: 10.1016/j.jmr.2019.07.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Distance determination by Electron Paramagnetic Resonance (EPR) based on measurements of the dipolar coupling are technically challenging for electron spin systems with broad spectra due to comparatively narrow microwave pulse excitation bandwidths. With Na4[{CuII(PyMTA)}-(stiff spacer)-{CuII(PyMTA)}] as a model compound, we compared DEER and RIDME measurements and investigated the use of frequency-swept pulses. We found very large improvements in sensitivity when substituting the monochromatic pump pulse by a frequency-swept one in DEER experiments with monochromatic observer pulses. This effect was especially strong in X band, where nearly the whole spectrum can be included in the experiment. The RIDME experiment is characterised by a trade-off in signal intensity and modulation depth. Optimal parameters are further influenced by varying steepness of the background decay. A simple 2-point optimization experiment was found to serve as good estimate to identify the mixing time of highest sensitivity. Using frequency-swept pulses in the observer sequences resulted in lower SNR in both the RIDME and the DEER experiment. Orientation selectivity was found to vary in both experiments with the detection position as well as with the settings of the pump pulse in DEER. In RIDME, orientation selection by relaxation anisotropy of the inverted spin appeared to be negligible as form factors remain relatively constant with varying mixing time. This reduces the overall observed orientation selection to the one given by the detection position. Field-averaged data from RIDME and DEER with a shaped pump pulse resulted in the same dipolar spectrum. We found that both methods have their advantages and disadvantages for given instrumental limitations and sample properties. Thus the choice of method depends on the situation at hand and we discuss which parameters should be considered for optimization.
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Affiliation(s)
- Frauke D Breitgoff
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland.
| | - Katharina Keller
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland.
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Daniel Klose
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
| | - Maxim Yulikov
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Gunnar Jeschke
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
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19
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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: 5.2] [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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20
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Wilson MD, Renault L, Maskell DP, Ghoneim M, Pye VE, Nans A, Rueda DS, Cherepanov P, Costa A. Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer. Nat Commun 2019; 10:4189. [PMID: 31519882 PMCID: PMC6744463 DOI: 10.1038/s41467-019-12007-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/08/2019] [Indexed: 01/02/2023] Open
Abstract
Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the histone octamer at the site of integration. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. The structural data along with complementary single-molecule Förster resonance energy transfer measurements reveal twisting and sliding of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA by approximately two base pairs along the histone octamer accommodates the necessary DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for nucleosomal DNA repositioning, bearing unexpected similarities to chromatin remodelers. Retroviral integrases catalyze the insertion of viral DNA into the host cell DNA and can use nucleosomes as substrates for integration. Here the authors present the 3.9 Å cryo-EM structure of prototype foamy virus integrase after strand transfer into nucleosomal DNA, which together with single-molecule FRET measurements provides evidence for a DNA looping and sliding mechanism of integrases.
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Affiliation(s)
- Marcus D Wilson
- Macromolecular Machines Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Ludovic Renault
- Macromolecular Machines Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.,NeCEN, University of Leiden, 2333CC, Leiden, Netherlands
| | - Daniel P Maskell
- Chromatin structure and mobile DNA Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Faculty of Biological Sciences, Leeds, LS2 9JT, UK
| | - Mohamed Ghoneim
- Single Molecule Imaging Group, MRC London Institute for Medical Science, London, W12 0NN, UK.,Molecular Virology, Department of Medicine, Imperial College London, London, W12 0NN, UK
| | - Valerie E Pye
- Chromatin structure and mobile DNA Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, NW1 1AT, UK
| | - David S Rueda
- Single Molecule Imaging Group, MRC London Institute for Medical Science, London, W12 0NN, UK. .,Molecular Virology, Department of Medicine, Imperial College London, London, W12 0NN, UK.
| | - Peter Cherepanov
- Chromatin structure and mobile DNA Laboratory, The Francis Crick Institute, London, NW1 1AT, UK. .,Department of Medicine, Imperial College London, St-Mary's Campus, Norfolk Place, London, W2 1PG, UK.
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.
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21
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Peter MF, Tuukkanen AT, Heubach CA, Selsam A, Duthie FG, Svergun DI, Schiemann O, Hagelueken G. Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology. Structure 2019; 27:1416-1426.e3. [DOI: 10.1016/j.str.2019.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/08/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
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22
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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: 18] [Impact Index Per Article: 3.0] [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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23
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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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24
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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: 66] [Impact Index Per Article: 11.0] [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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25
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Nucleosome remodelling: structural insights into ATP-dependent remodelling enzymes. Essays Biochem 2019; 63:45-58. [PMID: 30967479 DOI: 10.1042/ebc20180059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/22/2022]
Abstract
ATP-dependent chromatin remodelling enzymes play a fundamental role in determining how nucleosomes are organised, and render DNA sequences accessible to interacting proteins, thereby enabling precise regulation of eukaryotic genes. Remodelers conserved from yeast to humans are classified into four families based on the domains and motifs present in their ATPase subunits. Insights into overall assembly and the mode of interaction to the nucleosome by these different families of remodelers remained limited due to the complexity of obtaining structural information on these challenging samples. Electron microscopy and single-particle methods have made advancement and uncovered vital structural information on the number of remodelling complexes. In this article, we highlight some of the recent structural work that advanced our understanding on the mechanisms and biological functions of these ATP-dependent remodelling machines.
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26
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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: 69] [Impact Index Per Article: 11.5] [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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27
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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: 13] [Impact Index Per Article: 2.2] [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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28
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Zhou K, Gaullier G, Luger K. Nucleosome structure and dynamics are coming of age. Nat Struct Mol Biol 2018; 26:3-13. [PMID: 30532059 DOI: 10.1038/s41594-018-0166-x] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022]
Abstract
Since the first high-resolution structure of the nucleosome was reported in 1997, the available information on chromatin structure has increased very rapidly. Here, we review insights derived from cutting-edge biophysical and structural approaches applied to the study of nucleosome dynamics and nucleosome-binding factors, with a focus on the experimental advances driving the research. In addition, we highlight emerging challenges in nucleosome structural biology.
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Affiliation(s)
- Keda Zhou
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Guillaume Gaullier
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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29
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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: 59] [Impact Index Per Article: 8.4] [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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30
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Kovač K, Sauer A, Mačinković I, Awe S, Finkernagel F, Hoffmeister H, Fuchs A, Müller R, Rathke C, Längst G, Brehm A. Tumour-associated missense mutations in the dMi-2 ATPase alters nucleosome remodelling properties in a mutation-specific manner. Nat Commun 2018; 9:2112. [PMID: 29844320 PMCID: PMC5974244 DOI: 10.1038/s41467-018-04503-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/30/2018] [Indexed: 12/20/2022] Open
Abstract
ATP-dependent chromatin remodellers are mutated in more than 20% of human cancers. The consequences of these mutations on enzyme function are poorly understood. Here, we characterise the effects of CHD4 mutations identified in endometrial carcinoma on the remodelling properties of dMi-2, the highly conserved Drosophila homologue of CHD4. Mutations from different patients have surprisingly diverse defects on nucleosome binding, ATPase activity and nucleosome remodelling. Unexpectedly, we identify both mutations that decrease and increase the enzyme activity. Our results define the chromodomains and a novel regulatory region as essential for nucleosome remodelling. Genetic experiments in Drosophila demonstrate that expression of cancer-derived dMi-2 mutants misregulates differentiation of epithelial wing structures and produces phenotypes that correlate with their nucleosome remodelling properties. Our results help to define the defects of CHD4 in cancer at the mechanistic level and provide the basis for the development of molecular approaches aimed at restoring their activity. ATP-dependent chromatin remodelers are often found mutated in human cancers. Here, the authors characterize the nucleosome remodelling properties of cancer-associated mutants of the Drosophila Chd4 homolog dMi-2.
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Affiliation(s)
- Kristina Kovač
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Anja Sauer
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Igor Mačinković
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Stephan Awe
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Florian Finkernagel
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany.,Center for Tumour Biology and Immunology, University of Marburg, 35043, Marburg, Germany
| | - Helen Hoffmeister
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Andreas Fuchs
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Rolf Müller
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany.,Center for Tumour Biology and Immunology, University of Marburg, 35043, Marburg, Germany
| | - Christina Rathke
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, 35043, Marburg, Germany
| | - Gernot Längst
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Alexander Brehm
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany.
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31
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Winger J, Nodelman IM, Levendosky RF, Bowman GD. A twist defect mechanism for ATP-dependent translocation of nucleosomal DNA. eLife 2018; 7:34100. [PMID: 29809147 PMCID: PMC6031429 DOI: 10.7554/elife.34100] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/26/2018] [Indexed: 12/17/2022] Open
Abstract
As superfamily 2 (SF2)-type translocases, chromatin remodelers are expected to use an inchworm-type mechanism to walk along DNA. Yet how they move DNA around the histone core has not been clear. Here we show that a remodeler ATPase motor can shift large segments of DNA by changing the twist and length of nucleosomal DNA at superhelix location 2 (SHL2). Using canonical and variant 601 nucleosomes, we find that the Saccharomyces cerevisiae Chd1 remodeler decreased DNA twist at SHL2 in nucleotide-free and ADP-bound states, and increased twist with transition state analogs. These differences in DNA twist allow the open state of the ATPase to pull in ~1 base pair (bp) by stabilizing a small DNA bulge, and closure of the ATPase to shift the DNA bulge toward the dyad. We propose that such formation and elimination of twist defects underlie the mechanism of nucleosome sliding by CHD-, ISWI-, and SWI/SNF-type remodelers. DNA is shaped like a spiral staircase, twisting around itself to create a double helix. This results in a long string-like molecule that needs to be carefully packaged to fit inside the cells of organisms as diverse as fungi or humans. This packaging process starts when a portion of DNA tightly wraps around a spool-like core of proteins called histones. The resulting structure is known as a nucleosome. Like the beads on a necklace, nucleosomes exist at regular intervals along DNA. The DNA sequence around the histones cannot be accessed by a cell, and so the nucleosomes need to be ‘shifted’ along DNA to free up the genetic information. Enzymes known as chromatin remodelers perform this role by binding to a nucleosome, and then using energy to fuel a change in their structure that makes them ‘crawl’ on DNA like an inchworm. During this process, chromatin remodelers slide nucleosomes along the DNA, but it was unclear how exactly the inchworm motions pushed DNA around the histones. Here, Winger et al. look into the details of this mechanism by focusing on the chromatin remodeler Chd1, which is conserved from yeast to humans. Experiments show that, first, the enzyme slightly untwists the DNA double helix; this untwisting causes the DNA to pucker a little on the nucleosome. The puckering creates tension and ‘pulls’ DNA towards the remodeler. Then, Chd1 changes its structure and twists DNA in the opposite direction, which forces the puckered DNA onto the other side of the remodeler. This extra bit of DNA then propagates around the rest of the nucleosome, like the wave created by flicking the end of a long rope. This sheds light on how these enzymes can ratchet DNA past the histones. As the gatekeepers of our genetic information, chromatin remodelers are key to the health of the cell – in fact, they are often affected in cancers. The work by Winger et al. creates a framework that will help to understand how exactly chromatin remodelers help cells access the genetic information that the body needs to function properly.
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Affiliation(s)
- Jessica Winger
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Robert F Levendosky
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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32
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Gamarra N, Johnson SL, Trnka MJ, Burlingame AL, Narlikar GJ. The nucleosomal acidic patch relieves auto-inhibition by the ISWI remodeler SNF2h. eLife 2018; 7:35322. [PMID: 29664398 PMCID: PMC5976439 DOI: 10.7554/elife.35322] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
ISWI family chromatin remodeling motors use sophisticated autoinhibition mechanisms to control nucleosome sliding. Yet how the different autoinhibitory domains are regulated is not well understood. Here we show that an acidic patch formed by histones H2A and H2B of the nucleosome relieves the autoinhibition imposed by the AutoN and the NegC regions of the human ISWI remodeler SNF2h. Further, by single molecule FRET we show that the acidic patch helps control the distance travelled per translocation event. We propose a model in which the acidic patch activates SNF2h by providing a landing pad for the NegC and AutoN auto-inhibitory domains. Interestingly, the INO80 complex is also strongly dependent on the acidic patch for nucleosome sliding, indicating that this substrate feature can regulate remodeling enzymes with substantially different mechanisms. We therefore hypothesize that regulating access to the acidic patch of the nucleosome plays a key role in coordinating the activities of different remodelers in the cell. Every human cell contains nearly two meters of DNA, which is carefully packaged to form a dense structure known as chromatin. The building block of chromatin is the nucleosome, a unit composed of a short section of DNA tightly wound up around a spool-like core of proteins called histones. The tight structure of the nucleosome prevents the cell from accessing and ‘reading’ the genes in the packaged DNA, effectively switching off these genes. So the exact placement of nucleosomes helps manage which genes are turned on. Changing the position of the nucleosomes can ‘free’ the DNA and make genes available to the cell. Enzymes called chromatin remodelers move nucleosomes around – for example, they can make the histone core slide on the DNA strand. However, it is still unclear how these enzymes recognize nucleosomes. Previous research indicates that many proteins bind to nucleosomes by using a surface on the histone proteins called the acidic patch. Could chromatin remodelers also work by interacting with this acidic patch? To address this further, Gamarra et al. investigate how a chromatin remodeler enzyme known as SNF2h interacts with a nucleosome. By default, SNF2h is inactive because two of its regions called AutoN and NegC act as brakes. The experiments show that the acidic patch helps to bypass this inactivation and switches on SNF2h. Gamarra et al. propose that, when SNF2h docks on to the nucleosome, the patch provides a landing pad for the AutoN and NegC modules; this interaction activates the enzyme, which can then start remodeling the nucleosome. However, another type of chromatin remodeler also uses the patch to interact with nucleosomes but it does not have the AutoN and NegC regions. This suggests that chromatin remodelers work with the acidic patch in different ways. Overall, the findings deepen our understanding of how DNA is packaged in cells, and how this process may go wrong and cause disease.
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Affiliation(s)
- Nathan Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Stephanie L Johnson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, 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
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33
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Structural basis for ATP-dependent chromatin remodelling by the INO80 complex. Nature 2018; 556:386-390. [PMID: 29643509 PMCID: PMC6071913 DOI: 10.1038/s41586-018-0029-y] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/16/2018] [Indexed: 01/26/2023]
Abstract
DNA in the eukaryotic nucleus is packaged in the form of nucleosomes, ~147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP dependent chromatin remodelers1–3 such as the 15 subunit INO80 complex4. INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, exchanging histone H2A.Z with H2A, and positioning +1 and -1 nucleosomes at promoter DNA5–8. A structure and mechanism for these remodeling reactions is lacking. Here we report the cryo-electron microscopy structure at 4.3Å resolution, with parts at 3.7Å, of an evolutionary conserved core INO80 complex from Chaetomium thermophilum bound to a nucleosome. INO80core cradles one entire gyre of the nucleosome through multivalent DNA and histone contacts. A Rvb1/2 AAA+ ATPase hetero-hexamer is an assembly scaffold for the complex and acts as stator for the motor and nucleosome gripping subunits. The Swi2/Snf2 ATPase motor binds to SHL-6, unwraps ~15 base pairs, disrupts the H2A:DNA contacts and is poised to pump entry DNA into the nucleosome. Arp5-Ies6 grip SHL-2/-3 acting as counter grip for the motor on the other side of the H2A/H2B dimer. The Arp5 insertion domain forms a grappler element that binds the nucleosome dyad, connects the Arp5 core and entry DNA over a distance of ~90Å and packs against histone H2A/H2B near the acidic patch. Our structure together with biochemical data8 suggest a unified mechanism for nucleosome sliding and histone editing by INO80. The motor pumps entry DNA across H2A/H2B against Arp5 and the grappler, sliding nucleosomes as a ratchet. Transient exposure of H2A/H2B by the motor and differential recognition of H2A.Z and H2A may regulate histone exchange during translocation.
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34
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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: 138] [Impact Index Per Article: 19.7] [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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35
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The contribution of modern EPR to structural biology. Emerg Top Life Sci 2018; 2:9-18. [PMID: 33525779 PMCID: PMC7288997 DOI: 10.1042/etls20170143] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/22/2017] [Accepted: 01/02/2018] [Indexed: 02/08/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron–electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.
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36
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Harrer N, Schindler CEM, Bruetzel LK, Forné I, Ludwigsen J, Imhof A, Zacharias M, Lipfert J, Mueller-Planitz F. Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling. Structure 2018; 26:282-294.e6. [PMID: 29395785 DOI: 10.1016/j.str.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 10/25/2017] [Accepted: 12/27/2017] [Indexed: 11/17/2022]
Abstract
Chromatin remodeling factors assume critical roles by regulating access to nucleosomal DNA. To determine the architecture of the Drosophila ISWI remodeling enzyme, we developed an integrative structural approach that combines protein cross-linking, mass spectrometry, small-angle X-ray scattering, and computational modeling. The resulting structural model shows the ATPase module in a resting state with both ATPase lobes twisted against each other, providing support for a conformation that was recently trapped by crystallography. The autoinhibiting NegC region does not protrude from the ATPase module as suggested previously. The regulatory NTR domain is located near both ATPase lobes. The full-length enzyme is flexible and can adopt a compact structure in solution with the C-terminal HSS domain packing against the ATPase module. Our data imply a series of conformational changes upon activation of the enzyme and illustrate how the NTR, NegC, and HSS domains contribute to regulation of the ATPase module.
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Affiliation(s)
- Nadine Harrer
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Christina E M Schindler
- Physics Department (T38), Technical University of Munich, 85748 Garching, Germany; Center for Integrated Protein Science Munich, 81377 Munich, Germany
| | - Linda K Bruetzel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, 80799 Munich, Germany
| | - Ignasi Forné
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Johanna Ludwigsen
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Axel Imhof
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany
| | - Martin Zacharias
- Physics Department (T38), Technical University of Munich, 85748 Garching, Germany; Center for Integrated Protein Science Munich, 81377 Munich, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, 80799 Munich, Germany.
| | - Felix Mueller-Planitz
- Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, 82152 Martinsried, Germany.
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37
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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: 1.3] [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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38
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Blossey R, Schiessel H. The Latest Twists in Chromatin Remodeling. Biophys J 2018; 114:2255-2261. [PMID: 29310890 DOI: 10.1016/j.bpj.2017.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/09/2017] [Accepted: 12/12/2017] [Indexed: 02/03/2023] Open
Abstract
In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation. There are three regulatory levels of relevance that can be distinguished for this process: the intrinsic sequence preference of the histone octamer, which rules the positioning of the nucleosome along the DNA, notably in relation to the genetic information coded in DNA; the recognition or selection of nucleosomal substrates by remodeling complexes; and, finally, the motor action on the nucleosome exerted by the chromatin remodeler. Recent work has been able to provide crucial insights at each of these three levels that add new twists to this exciting and unfinished story, which we highlight in this perspective.
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Affiliation(s)
- Ralf Blossey
- University of Lille 1, Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, Lille, France.
| | - Helmut Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University, Leiden, the Netherlands
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39
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Nucleosome-Chd1 structure and implications for chromatin remodelling. Nature 2017; 550:539-542. [PMID: 29019976 PMCID: PMC5697743 DOI: 10.1038/nature24046] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/30/2017] [Indexed: 12/16/2022]
Abstract
Chromatin remodelling factors change nucleosome positioning and
facilitate DNA transcription, replication, and repair1. The conserved remodelling factor Chd12 can shift nucleosomes and induce a regular
nucleosome spacing3–5. Chd1 is required for RNA polymerase II
passage through nucleosomes6 and for
cellular pluripotency7. Chd1 contains the
DNA-binding domains SANT and SLIDE, a bilobal motor domain that hydrolyses
adenosine triphosphate (ATP), and a regulatory double chromodomain. Here we
report the cryo-electron microscopy (cryo-EM) structure of Chd1 from the yeast
S. cerevisiae bound to a nucleosome at a resolution of 4.8
Å. Chd1 detaches two turns of DNA from the histone octamer and binds
between the two DNA gyres in a state poised for catalysis. The SANT and SLIDE
domains contact detached DNA around superhelical location (SHL) -7 of the first
DNA gyre. The ATPase motor binds the second DNA gyre at SHL +2 and is anchored
to the N-terminal tail of histone H4 as in a recent nucleosome-Snf2 ATPase
structure8. Comparison with published
results9 reveals that the double
chromodomain swings towards nucleosomal DNA at SHL +1, resulting in ATPase
closure. The ATPase can then promote translocation of DNA towards the nucleosome
dyad, thereby loosening the first DNA gyre and remodelling the nucleosome.
Translocation may involve ratcheting of the two lobes of the ATPase, which is
trapped in a pre- or post-translocated state in the absence8 or presence, respectively, of transition state-mimicking
compounds.
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40
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Qiu Y, Levendosky RF, Chakravarthy S, Patel A, Bowman GD, Myong S. The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer. Mol Cell 2017; 68:76-88.e6. [PMID: 28943314 PMCID: PMC5745159 DOI: 10.1016/j.molcel.2017.08.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/30/2017] [Accepted: 08/18/2017] [Indexed: 11/18/2022]
Abstract
Chromatin remodelers catalyze dynamic packaging of the genome by carrying out nucleosome assembly/disassembly, histone exchange, and nucleosome repositioning. Remodeling results in evenly spaced nucleosomes, which requires probing both sides of the nucleosome, yet the way remodelers organize sliding activity to achieve this task is not understood. Here, we show that the monomeric Chd1 remodeler shifts DNA back and forth by dynamically alternating between different segments of the nucleosome. During sliding, Chd1 generates unstable remodeling intermediates that spontaneously relax to a pre-remodeled position. We demonstrate that nucleosome sliding is tightly controlled by two regulatory domains: the DNA-binding domain, which interferes with sliding when its range is limited by a truncated linking segment, and the chromodomains, which play a key role in substrate discrimination. We propose that active interplay of the ATPase motor with the regulatory domains may promote dynamic nucleosome structures uniquely suited for histone exchange and chromatin reorganization during transcription.
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Affiliation(s)
- Yupeng Qiu
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA
| | - Robert F Levendosky
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Ashok Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Gregory D Bowman
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL 61801, USA.
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41
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Feng W, Shao C, Liu HK. Versatile Roles of the Chromatin Remodeler CHD7 during Brain Development and Disease. Front Mol Neurosci 2017; 10:309. [PMID: 29033785 PMCID: PMC5625114 DOI: 10.3389/fnmol.2017.00309] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/14/2017] [Indexed: 11/13/2022] Open
Abstract
CHD7 (Chromo-Helicase-DNA binding protein 7) protein is an ATP-dependent chromatin remodeler. Heterozygous mutation of the CHD7 gene causes a severe congenital disease known as CHARGE syndrome. Most CHARGE syndrome patients have brain structural anomalies, implicating an important role of CHD7 during brain development. In this review, we summarize studies dissecting developmental functions of CHD7 in the brain and discuss pathogenic mechanisms behind neurodevelopmental defects caused by mutation of CHD7. As we discussed, CHD7 protein exhibits a remarkably specific and dynamic expression pattern in the brain. Studies in human and animal models have revealed that CHD7 is involved in multiple developmental lineages and processes in the brain. Mechanistically, CHD7 is essential for neural differentiation due to its transcriptional regulation in progenitor cells.
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Affiliation(s)
- Weijun Feng
- Division of Molecular Neurogenetics, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Chunxuan Shao
- Division of Molecular Neurogenetics, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Hai-Kun Liu
- Division of Molecular Neurogenetics, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
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