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Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L. Resolution of transcription-induced hexasome-nucleosome complexes by Chd1 and FACT. Mol Cell 2024:S1097-2765(24)00699-3. [PMID: 39270644 DOI: 10.1016/j.molcel.2024.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/07/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024]
Abstract
To maintain the nucleosome organization of transcribed genes, ATP-dependent chromatin remodelers collaborate with histone chaperones. Here, we show that at the 5' ends of yeast genes, RNA polymerase II (RNAPII) generates hexasomes that occur directly adjacent to nucleosomes. The resulting hexasome-nucleosome complexes are then resolved by Chd1. We present two cryoelectron microscopy (cryo-EM) structures of Chd1 bound to a hexasome-nucleosome complex before and after restoration of the missing inner H2A/H2B dimer by FACT. Chd1 uniquely interacts with the complex, positioning its ATPase domain to shift the hexasome away from the nucleosome. In the absence of the inner H2A/H2B dimer, its DNA-binding domain (DBD) packs against the ATPase domain, suggesting an inhibited state. Restoration of the dimer by FACT triggers a rearrangement that displaces the DBD and stimulates Chd1 remodeling. Our results demonstrate how chromatin remodelers interact with a complex nucleosome assembly and suggest how Chd1 and FACT jointly support transcription by RNAPII.
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Affiliation(s)
- Maik Engeholm
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany.
| | - Johann J Roske
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Elisa Oberbeckmann
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Michael Lidschreiber
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany.
| | - Lucas Farnung
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany; Harvard Medical School, Blavatnik Institute, Department of Cell Biology, 240 Longwood Avenue, Boston, MA 02115, USA.
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2
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Routhier E, Joubert A, Westbrook A, Pierre E, Lancrey A, Cariou M, Boulé JB, Mozziconacci J. In silico design of DNA sequences for in vivo nucleosome positioning. Nucleic Acids Res 2024; 52:6802-6810. [PMID: 38828788 PMCID: PMC11229325 DOI: 10.1093/nar/gkae468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/24/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
The computational design of synthetic DNA sequences with designer in vivo properties is gaining traction in the field of synthetic genomics. We propose here a computational method which combines a kinetic Monte Carlo framework with a deep mutational screening based on deep learning predictions. We apply our method to build regular nucleosome arrays with tailored nucleosomal repeat lengths (NRL) in yeast. Our design was validated in vivo by successfully engineering and integrating thousands of kilobases long tandem arrays of computationally optimized sequences which could accommodate NRLs much larger than the yeast natural NRL (namely 197 and 237 bp, compared to the natural NRL of ∼165 bp). RNA-seq results show that transcription of the arrays can occur but is not driven by the NRL. The computational method proposed here delineates the key sequence rules for nucleosome positioning in yeast and should be easily applicable to other sequence properties and other genomes.
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Affiliation(s)
- Etienne Routhier
- Laboratoire de Physique Théorique, CNRS, Sorbonne Université, Paris, France de la Matière Condensée, CNRS, Sorbonne Université, Paris, France
| | - Alexandra Joubert
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, CNRS, INSERM, Paris, France
| | - Alex Westbrook
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, CNRS, INSERM, Paris, France
| | - Edgard Pierre
- Laboratoire de Physique Théorique, CNRS, Sorbonne Université, Paris, France de la Matière Condensée, CNRS, Sorbonne Université, Paris, France
| | - Astrid Lancrey
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, CNRS, INSERM, Paris, France
| | - Marie Cariou
- Acquisition et Analyse de données pour l’histoire naturelle, Museum National d’Histoire Naturelle, CNRS, Paris, France
| | - Jean-Baptiste Boulé
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, CNRS, INSERM, Paris, France
| | - Julien Mozziconacci
- Laboratoire de Physique Théorique, CNRS, Sorbonne Université, Paris, France de la Matière Condensée, CNRS, Sorbonne Université, Paris, France
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, CNRS, INSERM, Paris, France
- Acquisition et Analyse de données pour l’histoire naturelle, Museum National d’Histoire Naturelle, CNRS, Paris, France
- Institut Universitaire de France, Paris, France
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3
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Gao ZX, He T, Zhang P, Hu X, Ge M, Xu YQ, Wang P, Pan HF. Epigenetic regulation of immune cells in systemic lupus erythematosus: insight from chromatin accessibility. Expert Opin Ther Targets 2024; 28:637-649. [PMID: 38943564 DOI: 10.1080/14728222.2024.2375372] [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: 03/19/2024] [Accepted: 06/28/2024] [Indexed: 07/01/2024]
Abstract
INTRODUCTION Systemic Lupus Erythematosus (SLE) is a multi-dimensional autoimmune disease involving numerous tissues throughout the body. The chromatin accessibility landscapes in immune cells play a pivotal role in governing their activation, function, and differentiation. Aberrant modulation of chromatin accessibility in immune cells is intimately associated with the onset and progression of SLE. AREAS COVERED In this review, we described the chromatin accessibility landscapes in immune cells, summarized the recent evidence of chromatin accessibility related to the pathogenesis of SLE, and discussed the potential of chromatin accessibility as a valuable option to identify novel therapeutic targets for this disease. EXPERT OPINION Dynamic changes in chromatin accessibility are intimately related to the pathogenesis of SLE and have emerged as a new direction for exploring its epigenetic mechanisms. The differently accessible chromatin regions in immune cells often contain binding sites for transcription factors (TFs) and cis-regulatory elements such as enhancers and promoters, which may be potential therapeutic targets for SLE. Larger scale cohort studies and integrating epigenomic, transcriptomic, and metabolomic data can provide deeper insights into SLE chromatin biology in the future.
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Affiliation(s)
- Zhao-Xing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Tian He
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xiao Hu
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Man Ge
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-Qing Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Wang
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
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Fouziya S, Krietenstein N, Mir US, Mieczkowski J, Khan MA, Baba A, Dar MA, Altaf M, Wani AH. Genome wide nucleosome landscape shapes 3D chromatin organization. SCIENCE ADVANCES 2024; 10:eadn2955. [PMID: 38848364 PMCID: PMC11160460 DOI: 10.1126/sciadv.adn2955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
The hierarchical chromatin organization begins with formation of nucleosomes, which fold into chromatin domains punctuated by boundaries and ultimately chromosomes. In a hierarchal organization, lower levels shape higher levels. However, the dependence of higher-order 3D chromatin organization on the nucleosome-level organization has not been studied in cells. We investigated the relationship between nucleosome-level organization and higher-order chromatin organization by perturbing nucleosomes across the genome by deleting Imitation SWItch (ISWI) and Chromodomain Helicase DNA-binding (CHD1) chromatin remodeling factors in budding yeast. We find that changes in nucleosome-level properties are accompanied by changes in 3D chromatin organization. Short-range chromatin contacts up to a few kilo-base pairs decrease, chromatin domains weaken, and boundary strength decreases. Boundary strength scales with accessibility and moderately with width of nucleosome-depleted region. Change in nucleosome positioning seems to alter the stiffness of chromatin, which can affect formation of chromatin contacts. Our results suggest a biomechanical "bottom-up" mechanism by which nucleosome distribution across genome shapes 3D chromatin organization.
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Affiliation(s)
- Shah Fouziya
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Nils Krietenstein
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
| | - Ulfat Syed Mir
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, J&K, 190006, India
| | - Jakub Mieczkowski
- International Research Agenda 3P Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
| | - Masood A. Khan
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Aemon Baba
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mohmmad Abaas Dar
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mohammad Altaf
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, J&K, 190006, India
| | - Ajazul H. Wani
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, 190006, India
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5
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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6
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Oberbeckmann E, Oudelaar AM. Genome organization across scales: mechanistic insights from in vitro reconstitution studies. Biochem Soc Trans 2024; 52:793-802. [PMID: 38451192 PMCID: PMC11088924 DOI: 10.1042/bst20230883] [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: 01/12/2024] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Eukaryotic genomes are compacted and organized into distinct three-dimensional (3D) structures, which range from small-scale nucleosome arrays to large-scale chromatin domains. These chromatin structures play an important role in the regulation of transcription and other nuclear processes. The molecular mechanisms that drive the formation of chromatin structures across scales and the relationship between chromatin structure and function remain incompletely understood. Because the processes involved are complex and interconnected, it is often challenging to dissect the underlying principles in the nuclear environment. Therefore, in vitro reconstitution systems provide a valuable approach to gain insight into the molecular mechanisms by which chromatin structures are formed and to determine the cause-consequence relationships between the processes involved. In this review, we give an overview of in vitro approaches that have been used to study chromatin structures across scales and how they have increased our understanding of the formation and function of these structures. We start by discussing in vitro studies that have given insight into the mechanisms of nucleosome positioning. Next, we discuss recent efforts to reconstitute larger-scale chromatin domains and loops and the resulting insights into the principles of genome organization. We conclude with an outlook on potential future applications of chromatin reconstitution systems and how they may contribute to answering open questions concerning chromatin architecture.
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Affiliation(s)
- Elisa Oberbeckmann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - A. Marieke Oudelaar
- Genome Organization and Regulation, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
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7
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Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Nat Rev Mol Cell Biol 2024; 25:309-332. [PMID: 38081975 DOI: 10.1038/s41580-023-00683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 03/28/2024]
Abstract
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re)arrange nucleosomes at the first level of chromatin organization. Their Snf2-type motor ATPases alter histone-DNA interactions through a common DNA translocation mechanism. Whether remodeller activities mainly catalyse nucleosome dynamics or accurately co-determine nucleosome organization remained unclear. In this Review, we discuss the emerging mechanisms of chromatin remodelling: dynamic remodeller architectures and their interactions, the inner workings of the ATPase cycle, allosteric regulation and pathological dysregulation. Recent mechanistic insights argue for a decisive role of remodellers in the energy-driven self-organization of chromatin, which enables both stability and plasticity of genome regulation - for example, during development and stress. Different remodellers, such as members of the SWI/SNF, ISWI, CHD and INO80 families, process (epi)genetic information through specific mechanisms into distinct functional outputs. Combinatorial assembly of remodellers and their interplay with histone modifications, histone variants, DNA sequence or DNA-bound transcription factors regulate nucleosome mobilization or eviction or histone exchange. Such input-output relationships determine specific nucleosome positions and compositions with distinct DNA accessibilities and mediate differential genome regulation. Finally, remodeller genes are often mutated in diseases characterized by genome dysregulation, notably in cancer, and we discuss their physiological relevance.
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Affiliation(s)
- Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Avinash B Patel
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Faculty of Chemistry and Pharmacy, LMU Munich, Munich, Germany
| | - Yuan He
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, LMU Munich, Martinsried, Germany.
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8
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Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z. Structure of the ISW1a complex bound to the dinucleosome. Nat Struct Mol Biol 2024; 31:266-274. [PMID: 38177688 DOI: 10.1038/s41594-023-01174-6] [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: 04/13/2022] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin organization and gene expression. Here we report the cryo-EM structure of chromatin remodeler ISW1a complex from Saccharomyces cerevisiae bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, while the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a and add a new mode of nucleosome remodeling in the context of a chromatin environment.
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Affiliation(s)
- Lifei Li
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Kangjing Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Youyang Sia
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Pengjing Hu
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Youpi Ye
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Zhucheng Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China.
- School of Life Science, Tsinghua University, Beijing, P.R. China.
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China.
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China.
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9
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Boltengagen M, Verhagen D, Wolff MR, Oberbeckmann E, Hanke M, Gerland U, Korber P, Mueller-Planitz F. A single fiber view of the nucleosome organization in eukaryotic chromatin. Nucleic Acids Res 2024; 52:166-185. [PMID: 37994698 PMCID: PMC10783498 DOI: 10.1093/nar/gkad1098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 10/13/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023] Open
Abstract
Eukaryotic cells are thought to arrange nucleosomes into extended arrays with evenly spaced nucleosomes phased at genomic landmarks. Here we tested to what extent this stereotypic organization describes the nucleosome organization in Saccharomyces cerevisiae using Fiber-Seq, a long-read sequencing technique that maps entire nucleosome arrays on individual chromatin fibers in a high throughput manner. With each fiber coming from a different cell, Fiber-Seq uncovers cell-to-cell heterogeneity. The long reads reveal the nucleosome architecture even over repetitive DNA such as the ribosomal DNA repeats. The absolute nucleosome occupancy, a parameter that is difficult to obtain with conventional sequencing approaches, is a direct readout of Fiber-Seq. We document substantial deviations from the stereotypical nucleosome organization with unexpectedly long linker DNAs between nucleosomes, gene bodies missing entire nucleosomes, cell-to-cell heterogeneity in nucleosome occupancy, heterogeneous phasing of arrays and irregular nucleosome spacing. Nucleosome array structures are indistinguishable throughout the gene body and with respect to the direction of transcription arguing against transcription promoting array formation. Acute nucleosome depletion destroyed most of the array organization indicating that nucleosome remodelers cannot efficiently pack nucleosomes under those conditions. Given that nucleosomes are cis-regulatory elements, the cell-to-cell heterogeneity uncovered by Fiber-Seq provides much needed information to understand chromatin structure and function.
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Affiliation(s)
- Mark Boltengagen
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Daan Verhagen
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Michael Roland Wolff
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Physics of Complex Biosystems, Physics Department, Technical University of Munich, Garching, Germany
| | - Elisa Oberbeckmann
- Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Matthias Hanke
- Physics of Complex Biosystems, Physics Department, Technical University of Munich, Garching, Germany
| | - Ulrich Gerland
- Physics of Complex Biosystems, Physics Department, Technical University of Munich, Garching, Germany
| | - Philipp Korber
- Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
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10
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Nishimura M, Fujii T, Tanaka H, Maehara K, Morishima K, Shimizu M, Kobayashi Y, Nozawa K, Takizawa Y, Sugiyama M, Ohkawa Y, Kurumizaka H. Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties. Commun Biol 2024; 7:61. [PMID: 38191828 PMCID: PMC10774305 DOI: 10.1038/s42003-023-05694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024] Open
Abstract
The nucleosome is a fundamental unit of chromatin in which about 150 base pairs of DNA are wrapped around a histone octamer. The overlapping di-nucleosome has been proposed as a product of chromatin remodeling around the transcription start site, and previously found as a chromatin unit, in which about 250 base pairs of DNA continuously bind to the histone core composed of a hexamer and an octamer. In the present study, our genome-wide analysis of human cells suggests another higher nucleosome stacking structure, the overlapping tri-nucleosome, which wraps about 300-350 base-pairs of DNA in the region downstream of certain transcription start sites of actively transcribed genes. We determine the cryo-electron microscopy (cryo-EM) structure of the overlapping tri-nucleosome, in which three subnucleosome moieties, hexasome, hexasome, and octasome, are associated by short connecting DNA segments. Small angle X-ray scattering and coarse-grained molecular dynamics simulation analyses reveal that the cryo-EM structure of the overlapping tri-nucleosome may reflect its structure in solution. Our findings suggest that nucleosome stacking structures composed of hexasome and octasome moieties may be formed by nucleosome remodeling factors around transcription start sites for gene regulation.
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Affiliation(s)
- Masahiro Nishimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, 111 TW, Alexander Drive, Research Triangle Park, NC, 27707, USA
| | - Takeru Fujii
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Hiroki Tanaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Yuki Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Kayo Nozawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan.
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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11
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Zeitler L, André K, Alberti A, Denby Wilkes C, Soutourina J, Goldar A. A genome-wide comprehensive analysis of nucleosome positioning in yeast. PLoS Comput Biol 2024; 20:e1011799. [PMID: 38266035 PMCID: PMC10843174 DOI: 10.1371/journal.pcbi.1011799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 02/05/2024] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
In eukaryotic cells, the one-dimensional DNA molecules need to be tightly packaged into the spatially constraining nucleus. Folding is achieved on its lowest level by wrapping the DNA around nucleosomes. Their arrangement regulates other nuclear processes, such as transcription and DNA repair. Despite strong efforts to study nucleosome positioning using Next Generation Sequencing (NGS) data, the mechanism of their collective arrangement along the gene body remains poorly understood. Here, we classify nucleosome distributions of protein-coding genes in Saccharomyces cerevisiae according to their profile similarity and analyse their differences using functional Principal Component Analysis. By decomposing the NGS signals into their main descriptive functions, we compared wild type and chromatin remodeler-deficient strains, keeping position-specific details preserved whilst considering the nucleosome arrangement as a whole. A correlation analysis with other genomic properties, such as gene size and length of the upstream Nucleosome Depleted Region (NDR), identified key factors that influence the nucleosome distribution. We reveal that the RSC chromatin remodeler-which is responsible for NDR maintenance-is indispensable for decoupling nucleosome arrangement within the gene from positioning outside, which interfere in rsc8-depleted conditions. Moreover, nucleosome profiles in chd1Δ strains displayed a clear correlation with RNA polymerase II presence, whereas wild type cells did not indicate a noticeable interdependence. We propose that RSC is pivotal for global nucleosome organisation, whilst Chd1 plays a key role for maintaining local arrangement.
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Affiliation(s)
- Leo Zeitler
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Kévin André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Adriana Alberti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
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12
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Converso C, Pierrakeas L, Chan L, Chowdhury S, Kuznetsov VI, Denu JM, Luk E. Nucleic acid sequence contributes to remodeler-mediated targeting of histone H2A.Z. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570360. [PMID: 38106078 PMCID: PMC10723385 DOI: 10.1101/2023.12.06.570360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The variant histone H2A.Z is inserted into nucleosomes immediately downstream of promoters and is important for transcription. The site-specific deposition of H2A.Z is catalyzed by SWR, a conserved chromatin remodeler with affinity for promoter-proximal nucleosome depleted regions (NDRs) and histone acetylation. By comparing the genomic distribution of H2A.Z in wild-type and SWR-deficient cells, we found that SWR is also responsible for depositing H2A.Z at thousands of non-canonical sites not directly linked to NDRs or histone acetylation. To understand the targeting mechanism of H2A.Z, we presented SWR with a library of nucleosomes isolated from yeast and characterized those preferred by SWR. We found that SWR prefers nucleosomes associated with intergenic over coding regions, especially when polyadenine tracks are present. Insertion of polyadenine sequences into recombinant nucleosomes near the H2A-H2B binding site stimulated the H2A.Z insertion activity of SWR. Therefore, the genome is encoded with information contributing to remodeler-mediated targeting of H2A.Z.
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13
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Robert F, Jeronimo C. Transcription-coupled nucleosome assembly. Trends Biochem Sci 2023; 48:978-992. [PMID: 37657993 DOI: 10.1016/j.tibs.2023.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
Eukaryotic transcription occurs on chromatin, where RNA polymerase II encounters nucleosomes during elongation. These nucleosomes must unravel for the DNA to enter the active site. However, in most transcribed genes, nucleosomes remain intact due to transcription-coupled chromatin assembly mechanisms. These mechanisms primarily involve the local reassembly of displaced nucleosomes to prevent (epi)genomic instability and the emergence of cryptic transcription. As a fail-safe mechanism, cells can assemble nucleosomes de novo, particularly in highly transcribed genes, but this may result in the loss of epigenetic information. This review examines transcription-coupled chromatin assembly, with an emphasis on studies in yeast and recent structural studies. These studies shed light on how elongation factors and histone chaperones coordinate to enable nucleosome recycling during transcription.
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Affiliation(s)
- François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada.
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
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14
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Litwin I, Nowicka M, Markowska K, Maciaszczyk-Dziubińska E, Tomaszewska P, Wysocki R, Kramarz K. ISW1a modulates cohesin distribution in centromeric and pericentromeric regions. Nucleic Acids Res 2023; 51:9101-9121. [PMID: 37486771 PMCID: PMC10516642 DOI: 10.1093/nar/gkad612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 06/28/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023] Open
Abstract
Cohesin is a highly conserved, multiprotein complex whose canonical function is to hold sister chromatids together to ensure accurate chromosome segregation. Cohesin association with chromatin relies on the Scc2-Scc4 cohesin loading complex that enables cohesin ring opening and topological entrapment of sister DNAs. To better understand how sister chromatid cohesion is regulated, we performed a proteomic screen in budding yeast that identified the Isw1 chromatin remodeler as a cohesin binding partner. In addition, we found that Isw1 also interacts with Scc2-Scc4. Lack of Isw1 protein, the Ioc3 subunit of ISW1a or Isw1 chromatin remodeling activity resulted in increased accumulation of cohesin at centromeres and pericentromeres, suggesting that ISW1a may promote efficient translocation of cohesin from the centromeric site of loading to neighboring regions. Consistent with the role of ISW1a in the chromatin organization of centromeric regions, Isw1 was found to be recruited to centromeres. In its absence we observed changes in the nucleosomal landscape at centromeres and pericentromeres. Finally, we discovered that upon loss of RSC functionality, ISW1a activity leads to reduced cohesin binding and cohesion defect. Taken together, our results support the notion of a key role of chromatin remodelers in the regulation of cohesin distribution on chromosomes.
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Affiliation(s)
- Ireneusz Litwin
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Małgorzata Nowicka
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Katarzyna Markowska
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubińska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Paulina Tomaszewska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Karol Kramarz
- Academic Excellence Hub - Research Centre for DNA Repair and Replication, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
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15
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Stefanova ME, Volokh OI, Chertkov OV, Armeev GA, Shaytan AK, Feofanov AV, Kirpichnikov MP, Sokolova OS, Studitsky VM. Structure and Dynamics of Compact Dinucleosomes: Analysis by Electron Microscopy and spFRET. Int J Mol Sci 2023; 24:12127. [PMID: 37569503 PMCID: PMC10419094 DOI: 10.3390/ijms241512127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Formation of compact dinucleosomes (CODIs) occurs after collision between adjacent nucleosomes at active regulatory DNA regions. Although CODIs are likely dynamic structures, their structural heterogeneity and dynamics were not systematically addressed. Here, single-particle Förster resonance energy transfer (spFRET) and electron microscopy were employed to study the structure and dynamics of CODIs. spFRET microscopy in solution and in gel revealed considerable uncoiling of nucleosomal DNA from the histone octamer in a fraction of CODIs, suggesting that at least one of the nucleosomes is destabilized in the presence of the adjacent closely positioned nucleosome. Accordingly, electron microscopy analysis suggests that up to 30 bp of nucleosomal DNA are involved in transient uncoiling/recoiling on the octamer. The more open and dynamic nucleosome structure in CODIs cannot be stabilized by histone chaperone Spt6. The data suggest that proper internucleosomal spacing is an important determinant of chromatin stability and support the possibility that CODIs could be intermediates of chromatin disruption.
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Affiliation(s)
- Maria E. Stefanova
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Olesya I. Volokh
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Oleg V. Chertkov
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Grigory A. Armeev
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Alexey K. Shaytan
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Alexey V. Feofanov
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
| | - Mikhail P. Kirpichnikov
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Olga S. Sokolova
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
- Biological Faculty, MSU-BIT Shenzhen University, Shenzhen 518115, China
| | - Vasily M. Studitsky
- Biology Faculty, Lomonosov Moscow State University, Moscow 119234, Russia; (M.E.S.); (O.I.V.); (O.V.C.); (G.A.A.); (A.K.S.); (A.V.F.); (O.S.S.); (V.M.S.)
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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16
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Wu H, Muñoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y. Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility. Science 2023; 381:319-324. [PMID: 37384669 PMCID: PMC10480058 DOI: 10.1126/science.adf4197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 06/17/2023] [Indexed: 07/01/2023]
Abstract
Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report structures of Saccharomyces cerevisiae INO80 bound to a hexasome or a nucleosome. INO80 binds the two substrates in substantially different orientations. On a hexasome, INO80 places its ATPase subunit, Ino80, at superhelical location -2 (SHL -2), in contrast to SHL -6 and SHL -7, as previously seen on nucleosomes. Our results suggest that INO80 action on hexasomes resembles action by other remodelers on nucleosomes such that Ino80 is maximally active near SHL -2. The SHL -2 position also plays a critical role for nucleosome remodeling by INO80. Overall, the mechanistic adaptations used by INO80 for preferential hexasome sliding imply that subnucleosomal particles play considerable regulatory roles.
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Affiliation(s)
- Hao Wu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elise N. Muñoz
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Laura J. Hsieh
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Un Seng Chio
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Muryam A. Gourdet
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA
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17
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Gvozdenov Z, Barcutean Z, Struhl K. Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells. Mol Cell 2023; 83:1786-1797.e5. [PMID: 37137302 PMCID: PMC10247422 DOI: 10.1016/j.molcel.2023.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/18/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
We measure transcriptional noise in yeast by analyzing chromatin structure and transcription of an 18-kb region of DNA whose sequence was randomly generated. Nucleosomes fully occupy random-sequence DNA, but nucleosome-depleted regions (NDRs) are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays. Steady-state levels of random-sequence RNAs are comparable to yeast mRNAs, although transcription and decay rates are higher. Transcriptional initiation from random-sequence DNA occurs at numerous sites, indicating very low intrinsic specificity of the RNA Pol II machinery. In contrast, poly(A) profiles of random-sequence RNAs are roughly comparable to those of yeast mRNAs, suggesting limited evolutionary restraints on poly(A) site choice. Random-sequence RNAs show higher cell-to-cell variability than yeast mRNAs, suggesting that functional elements limit variability. These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.
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Affiliation(s)
- Zlata Gvozdenov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zeno Barcutean
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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18
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Chacin E, Reusswig KU, Furtmeier J, Bansal P, Karl LA, Pfander B, Straub T, Korber P, Kurat CF. Establishment and function of chromatin organization at replication origins. Nature 2023; 616:836-842. [PMID: 37020028 DOI: 10.1038/s41586-023-05926-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/03/2023] [Indexed: 04/07/2023]
Abstract
The origin recognition complex (ORC) is essential for initiation of eukaryotic chromosome replication as it loads the replicative helicase-the minichromosome maintenance (MCM) complex-at replication origins1. Replication origins display a stereotypic nucleosome organization with nucleosome depletion at ORC-binding sites and flanking arrays of regularly spaced nucleosomes2-4. However, how this nucleosome organization is established and whether this organization is required for replication remain unknown. Here, using genome-scale biochemical reconstitution with approximately 300 replication origins, we screened 17 purified chromatin factors from budding yeast and found that the ORC established nucleosome depletion over replication origins and flanking nucleosome arrays by orchestrating the chromatin remodellers INO80, ISW1a, ISW2 and Chd1. The functional importance of the nucleosome-organizing activity of the ORC was demonstrated by orc1 mutations that maintained classical MCM-loader activity but abrogated the array-generation activity of ORC. These mutations impaired replication through chromatin in vitro and were lethal in vivo. Our results establish that ORC, in addition to its canonical role as the MCM loader, has a second crucial function as a master regulator of nucleosome organization at the replication origin, a crucial prerequisite for efficient chromosome replication.
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Affiliation(s)
- Erika Chacin
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Karl-Uwe Reusswig
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jessica Furtmeier
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Priyanka Bansal
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Leonhard A Karl
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
| | - Boris Pfander
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute of Genome Stability in Aging and Disease, CECAD, University of Cologne, Medical Faculty, Cologne, Germany
| | - Tobias Straub
- Core Facility Bioinformatics, BMC, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Philipp Korber
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Christoph F Kurat
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany.
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19
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Matabishi-Bibi L, Challal D, Barucco M, Libri D, Babour A. Termination of the unfolded protein response is guided by ER stress-induced HAC1 mRNA nuclear retention. Nat Commun 2022; 13:6331. [PMID: 36284099 PMCID: PMC9596429 DOI: 10.1038/s41467-022-34133-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
Cellular homeostasis is maintained by surveillance mechanisms that intervene at virtually every step of gene expression. In the nucleus, the yeast chromatin remodeler Isw1 holds back maturing mRNA ribonucleoparticles to prevent their untimely export, but whether this activity operates beyond quality control of mRNA biogenesis to regulate gene expression is unknown. Here, we identify the mRNA encoding the central effector of the unfolded protein response (UPR) HAC1, as an Isw1 RNA target. The direct binding of Isw1 to the 3' untranslated region of HAC1 mRNA restricts its nuclear export and is required for accurate UPR abatement. Accordingly, ISW1 inactivation sensitizes cells to endoplasmic reticulum (ER) stress while its overexpression reduces UPR induction. Our results reveal an unsuspected mechanism, in which binding of ER-stress induced Isw1 to HAC1 mRNA limits its nuclear export, providing a feedback loop that fine-tunes UPR attenuation to guarantee homeostatic adaptation to ER stress.
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Affiliation(s)
- Laura Matabishi-Bibi
- grid.508487.60000 0004 7885 7602Univ Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR7212, Hôpital St. Louis 1, Avenue Claude Vellefaux, 75475 Paris Cedex 10, France
| | - Drice Challal
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mara Barucco
- grid.461913.80000 0001 0676 2143Institut Jacques Monod, Univ Paris Diderot, Sorbonne Paris Cité, CNRS, Bâtiment Buffon, 15 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Domenico Libri
- grid.429192.50000 0004 0599 0285Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Anna Babour
- grid.508487.60000 0004 7885 7602Univ Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR7212, Hôpital St. Louis 1, Avenue Claude Vellefaux, 75475 Paris Cedex 10, France
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20
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Hendy O, Serebreni L, Bergauer K, Muerdter F, Huber L, Nemčko F, Stark A. Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers. Mol Cell 2022; 82:3598-3612.e7. [PMID: 36113480 PMCID: PMC7614073 DOI: 10.1016/j.molcel.2022.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/13/2022] [Accepted: 08/17/2022] [Indexed: 01/21/2023]
Abstract
Gene transcription is a highly regulated process in all animals. In Drosophila, two major transcriptional programs, housekeeping and developmental, have promoters with distinct regulatory compatibilities and nucleosome organization. However, it remains unclear how the differences in chromatin structure relate to the distinct regulatory properties and which chromatin remodelers are required for these programs. Using rapid degradation of core remodeler subunits in Drosophila melanogaster S2 cells, we demonstrate that developmental gene transcription requires SWI/SNF-type complexes, primarily to maintain distal enhancer accessibility. In contrast, wild-type-level housekeeping gene transcription requires the Iswi and Ino80 remodelers to maintain nucleosome positioning and phasing at promoters. These differential remodeler dependencies relate to different DNA-sequence-intrinsic nucleosome affinities, which favor a default ON state for housekeeping but a default OFF state for developmental gene transcription. Overall, our results demonstrate how different transcription-regulatory strategies are implemented by DNA sequence, chromatin structure, and remodeler activity.
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Affiliation(s)
- Oliver Hendy
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Leonid Serebreni
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Katharina Bergauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Felix Muerdter
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Lukas Huber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Filip Nemčko
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Medical University of Vienna, Vienna BioCenter (VBC), Vienna 1030, Austria.
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21
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Corcoran ET, LeBlanc C, Huang YC, Arias Tsang M, Sarkiss A, Hu Y, Pedmale UV, Jacob Y. Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time. THE PLANT CELL 2022; 34:3611-3631. [PMID: 35879829 PMCID: PMC9516085 DOI: 10.1093/plcell/koac211] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/15/2022] [Indexed: 06/13/2023]
Abstract
Despite the broad array of roles for epigenetic mechanisms on regulating diverse processes in eukaryotes, no experimental system is currently available in plants for the direct assessment of histone function. In this work, we present the development of a genetic strategy in Arabidopsis (Arabidopsis thaliana) whereby modified histone H4 transgenes can completely replace the expression of endogenous histone H4 genes. Accordingly, we established a collection of plants expressing different H4 point mutants targeting residues that may be post-translationally modified in vivo. To demonstrate its utility, we screened this new H4 mutant collection to uncover substitutions in H4 that alter flowering time. We identified different mutations in the H4 tail (H4R17A) and the H4 globular domain (H4R36A, H4R39K, H4R39A, and H4K44A) that strongly accelerate the floral transition. Furthermore, we identified a conserved regulatory relationship between H4R17 and the ISWI chromatin remodeling complex in plants: As with other biological systems, H4R17 regulates nucleosome spacing via ISWI. Overall, this work provides a large set of H4 mutants to the plant epigenetics community that can be used to systematically assess histone H4 function in Arabidopsis and a roadmap to replicate this strategy for studying other histone proteins in plants.
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Affiliation(s)
- Emma Tung Corcoran
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Chantal LeBlanc
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Yi-Chun Huang
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Mia Arias Tsang
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Anthony Sarkiss
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Yuzhao Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ullas V Pedmale
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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22
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Kondalaji SG, Bowman GD. In Vitro Mapping of Nucleosome Positions at Base-Pair Resolution Using Ortho-Phenanthroline. Curr Protoc 2022; 2:e518. [PMID: 35943282 PMCID: PMC9373710 DOI: 10.1002/cpz1.518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The positions of nucleosomes along genomic DNA play a role in defining patterns of gene expression and chromatin organization. Determination of nucleosome positions in vivo and in vitro, as revealed by the locations of histones on DNA, has provided insight into mechanisms of nucleosome sliding, spacing, assembly, and disassembly. Here, we describe methods for the in vitro determination of histone-DNA contacts at base-pair (bp) resolution. The protocol involves the labeling of histones with ortho-phenanthroline (OP), site-specific cleavage of nucleosomal DNA, and processing and analysis of the resulting DNA fragments. This methodology provides an efficient and high-resolution means for studying kinetics and behavior of enzymes that alter nucleosome structure and/or positioning, and can be used to identify preferred distributions of nucleosomes on natural DNA sequences. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Cysteine-specific chemical modification of folded histones with ortho-phenanthroline (OP) Basic Protocol 2: Nucleosome sliding assay adapted for OP mapping of histone-DNA contacts Basic Protocol 3: OP-mediated cleavage, processing, and analysis of DNA fragments using a sequencing gel Support Protocol 1: Preparation of dideoxy sequencing ladders Support Protocol 2: Preparation and running of a denaturing DNA sequencing gel.
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Affiliation(s)
| | - Gregory D Bowman
- T. C. Jenkins Department of Biophysics, Johns Hopkins
University, Baltimore, Maryland 21218
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23
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Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq. Stem Cell Reports 2022; 17:1730-1742. [PMID: 35750045 PMCID: PMC9287678 DOI: 10.1016/j.stemcr.2022.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) can reprogram terminally differentiated somatic cells into totipotent embryos, but with multiple defects. The nucleosome positioning, as an important epigenetic regulator for gene expression, is largely unexplored during SCNT embryonic development. Here, we mapped genome-wide nucleosome profiles in mouse SCNT embryos using ultra-low-input MNase-seq (ULI-MNase-seq). We found that the nucleosome-depleted regions (NDRs) around promoters underwent dramatic reestablishment, which is consistent with the cell cycle. Dynamics of nucleosome position in SCNT embryos were delayed compared to fertilized embryos. Subsequently, we found that the aberrant gene expression levels in inner cell mass (ICM) were positively correlated with promoter NDRs in donor cells, which indicated that the memory of nucleosome occupancy in donor cells was a potential barrier for SCNT-mediated reprogramming. We further confirmed that the histone acetylation level of donor cells was associated with the memory of promoter NDRs. Our study provides insight into nucleosome reconfiguration during SCNT preimplantation embryonic development.
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24
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Trujillo JT, Long J, Aboelnour E, Ogas J, Wisecaver JH. CHD chromatin remodeling protein diversification yields novel clades and domains absent in classic model organisms. Genome Biol Evol 2022; 14:6582301. [PMID: 35524943 PMCID: PMC9113485 DOI: 10.1093/gbe/evac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
Chromatin remodelers play a fundamental role in the assembly of chromatin, regulation of transcription, and DNA repair. Biochemical and functional characterizations of the CHD family of chromatin remodelers from a variety of model organisms have shown that these remodelers participate in a wide range of activities. However, because the evolutionary history of CHD homologs is unclear, it is difficult to predict which of these activities are broadly conserved and which have evolved more recently in individual eukaryotic lineages. Here, we performed a comprehensive phylogenetic analysis of 8,042 CHD homologs from 1,894 species to create a model for the evolution of this family across eukaryotes with a particular focus on the timing of duplications that gave rise to the diverse copies observed in plants, animals, and fungi. Our analysis confirms that the three major subfamilies of CHD remodelers originated in the eukaryotic last common ancestor, and subsequent losses occurred independently in different lineages. Improved taxon sampling identified several subfamilies of CHD remodelers in plants that were absent or highly divergent in the model plant Arabidopsis thaliana. Whereas the timing of CHD subfamily expansions in vertebrates corresponds to whole genome duplication events, the mechanisms underlying CHD diversification in land plants appear more complicated. Analysis of protein domains reveals that CHD remodeler diversification has been accompanied by distinct transitions in domain architecture, contributing to the functional differences observed between these remodelers. This study demonstrates the importance of proper taxon sampling when studying ancient evolutionary events to prevent misinterpretation of subsequent lineage-specific changes and provides an evolutionary framework for functional and comparative analysis of this critical chromatin remodeler family across eukaryotes.
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Affiliation(s)
- Joshua T Trujillo
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jiaxin Long
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Erin Aboelnour
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA.,Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Joseph Ogas
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jennifer H Wisecaver
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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25
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Mattola S, Salokas K, Aho V, Mäntylä E, Salminen S, Hakanen S, Niskanen EA, Svirskaite J, Ihalainen TO, Airenne KJ, Kaikkonen-Määttä M, Parrish CR, Varjosalo M, Vihinen-Ranta M. Parvovirus nonstructural protein 2 interacts with chromatin-regulating cellular proteins. PLoS Pathog 2022; 18:e1010353. [PMID: 35395063 PMCID: PMC9020740 DOI: 10.1371/journal.ppat.1010353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/20/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022] Open
Abstract
Autonomous parvoviruses encode at least two nonstructural proteins, NS1 and NS2. While NS1 is linked to important nuclear processes required for viral replication, much less is known about the role of NS2. Specifically, the function of canine parvovirus (CPV) NS2 has remained undefined. Here we have used proximity-dependent biotin identification (BioID) to screen for nuclear proteins that associate with CPV NS2. Many of these associations were seen both in noninfected and infected cells, however, the major type of interacting proteins shifted from nuclear envelope proteins to chromatin-associated proteins in infected cells. BioID interactions revealed a potential role for NS2 in DNA remodeling and damage response. Studies of mutant viral genomes with truncated forms of the NS2 protein suggested a change in host chromatin accessibility. Moreover, further studies with NS2 mutants indicated that NS2 performs functions that affect the quantity and distribution of proteins linked to DNA damage response. Notably, mutation in the splice donor site of the NS2 led to a preferred formation of small viral replication center foci instead of the large coalescent centers seen in wild-type infection. Collectively, our results provide insights into potential roles of CPV NS2 in controlling chromatin remodeling and DNA damage response during parvoviral replication. Parvoviruses are small, nonenveloped DNA viruses, that besides being noteworthy pathogens in many animal species, including humans, are also being developed as vectors for gene and cancer therapy. Canine parvovirus is an autonomously replicating parvovirus that encodes two nonstructural proteins, NS1 and NS2. NS1 is required for viral DNA replication and packaging, as well as gene expression. However, very little is known about the function of NS2. Our studies indicate that NS2 serves a previously undefined important function in chromatin modification and DNA damage responses. Therefore, it appears that although both NS1 and NS2 are needed for a productive infection they play very different roles in the process.
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Affiliation(s)
- Salla Mattola
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Kari Salokas
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Vesa Aho
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sami Salminen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Satu Hakanen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Einari A. Niskanen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Julija Svirskaite
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Teemu O. Ihalainen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kari J. Airenne
- Kuopio Center for Gene and Cell Therapy (KCT), Kuopio, Finland
| | | | - Colin R. Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, University of Cornell, Ithaca, New York, United States of America
| | - Markku Varjosalo
- Institute of Biotechnology and Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- * E-mail:
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26
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Acidic patch histone mutations and their effects on nucleosome remodeling. Biochem Soc Trans 2022; 50:907-919. [PMID: 35356970 DOI: 10.1042/bst20210773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 12/15/2022]
Abstract
Structural and biochemical studies have identified a histone surface on each side of the nucleosome disk termed 'the nucleosome acidic patch' that acts as a regulatory hub for the function of numerous nuclear proteins, including ATP-dependent chromatin complexes (remodelers). Four major remodeler subfamilies, SWI/SNF, ISWI, CHD, and INO80, have distinct modes of interaction with one or both nucleosome acidic patches, contributing to their specific remodeling outcomes. Genome-wide sequencing analyses of various human cancers have uncovered high-frequency mutations in histone coding genes, including some that map to the acidic patch. How cancer-related acidic patch histone mutations affect nucleosome remodeling is mainly unknown. Recent advances in in vitro chromatin reconstitution have enabled access to physiologically relevant nucleosomes, including asymmetric nucleosomes that possess both wild-type and acidic patch mutant histone copies. Biochemical investigation of these substrates revealed unexpected remodeling outcomes with far-reaching implications for alteration of chromatin structure. This review summarizes recent findings of how different remodeler families interpret wild-type and mutant acidic patches for their remodeling functions and discusses models for remodeler-mediated changes in chromatin landscapes as a consequence of acidic patch mutations.
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27
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Li J, Bergmann L, Rafael de Almeida A, Webb KM, Gogol M, Voigt P, Liu Y, Liang H, Smolle M. H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function. Nucleic Acids Res 2022; 50:2549-2565. [PMID: 35188579 PMCID: PMC8934638 DOI: 10.1093/nar/gkac077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 01/20/2022] [Accepted: 02/15/2022] [Indexed: 11/23/2022] Open
Abstract
The Isw1b chromatin-remodeling complex is specifically recruited to gene bodies to help retain pre-existing histones during transcription by RNA polymerase II. Recruitment is dependent on H3K36 methylation and the Isw1b subunit Ioc4, which contains an N-terminal PWWP domain. Here, we present the crystal structure of the Ioc4-PWWP domain, including a detailed functional characterization of the domain on its own as well as in the context of full-length Ioc4 and the Isw1b remodeler. The Ioc4-PWWP domain preferentially binds H3K36me3-containing nucleosomes. Its ability to bind DNA is required for nucleosome binding. It is also furthered by the unique insertion motif present in Ioc4-PWWP. The ability to bind H3K36me3 and DNA promotes the interaction of full-length Ioc4 with nucleosomes in vitro and they are necessary for its recruitment to gene bodies in vivo. Furthermore, a fully functional Ioc4-PWWP domain promotes efficient remodeling by Isw1b and the maintenance of ordered chromatin in vivo, thereby preventing the production of non-coding RNAs.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Lena Bergmann
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Andreia Rafael de Almeida
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Kimberly M Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Madelaine M Gogol
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Yingfang Liu
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- School of Medicine, Sun Yat-Sen University, Guangzhou 510275, China
| | - Huanhuan Liang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Michaela M Smolle
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
- BioPhysics Core Facility, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
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28
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Karl LA, Peritore M, Galanti L, Pfander B. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Front Genet 2022; 12:821543. [PMID: 35096025 PMCID: PMC8790285 DOI: 10.3389/fgene.2021.821543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.
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Affiliation(s)
- Leonhard Andreas Karl
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Peritore
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
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29
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Reb1, Cbf1, and Pho4 bias histone sliding and deposition away from their binding sites. Mol Cell Biol 2021; 42:e0047221. [PMID: 34898278 DOI: 10.1128/mcb.00472-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In transcriptionally active genes, nucleosome positions in promoters are regulated by nucleosome displacing factors (NDFs) and chromatin remodeling enzymes. Depletion of NDFs or the RSC chromatin remodeler shrinks or abolishes the nucleosome depleted regions (NDRs) in promoters, which can suppress gene activation and result in cryptic transcription. Despite their vital cellular functions, how the action of chromatin remodelers may be directly affected by site-specific binding factors like NDFs is poorly understood. Here we demonstrate that two NDFs, Reb1 and Cbf1, can direct both Chd1 and RSC chromatin remodeling enzymes in vitro, stimulating repositioning of the histone core away from their binding sites. Interestingly, although the Pho4 transcription factor had a much weaker effect on nucleosome positioning, both NDFs and Pho4 were able to similarly redirect positioning of hexasomes. In chaperone-mediated nucleosome assembly assays, Reb1 but not Pho4 showed an ability to block deposition of the histone H3/H4 tetramer, but Reb1 did not block addition of the H2A/H2B dimer to hexasomes. Our in vitro results show that NDFs bias the action of remodelers to increase the length of the free DNA in the vicinity of their binding sites. These results suggest that NDFs could directly affect NDR architecture through chromatin remodelers.
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30
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Singh AK, Schauer T, Pfaller L, Straub T, Mueller-Planitz F. The biogenesis and function of nucleosome arrays. Nat Commun 2021; 12:7011. [PMID: 34853297 PMCID: PMC8636622 DOI: 10.1038/s41467-021-27285-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/09/2021] [Indexed: 11/24/2022] Open
Abstract
Numerous chromatin remodeling enzymes position nucleosomes in eukaryotic cells. Aside from these factors, transcription, DNA sequence, and statistical positioning of nucleosomes also shape the nucleosome landscape. The precise contributions of these processes remain unclear due to their functional redundancy in vivo. By incisive genome engineering, we radically decreased their redundancy in Saccharomyces cerevisiae. The transcriptional machinery strongly disrupts evenly spaced nucleosomes. Proper nucleosome density and DNA sequence are critical for their biogenesis. The INO80 remodeling complex helps space nucleosomes in vivo and positions the first nucleosome over genes in an H2A.Z-independent fashion. INO80 requires its Arp8 subunit but unexpectedly not the Nhp10 module for spacing. Cells with irregularly spaced nucleosomes suffer from genotoxic stress including DNA damage, recombination and transpositions. We derive a model of the biogenesis of the nucleosome landscape and suggest that it evolved not only to regulate but also to protect the genome.
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Affiliation(s)
- Ashish Kumar Singh
- grid.5252.00000 0004 1936 973XMolecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany
| | - Tamás Schauer
- grid.5252.00000 0004 1936 973XBioinformatics Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany
| | - Lena Pfaller
- grid.5252.00000 0004 1936 973XMolecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany ,grid.419481.10000 0001 1515 9979Present Address: Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Tobias Straub
- grid.5252.00000 0004 1936 973XBioinformatics Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany
| | - Felix Mueller-Planitz
- Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany. .,Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
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31
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Uzun Ü, Brown T, Fischl H, Angel A, Mellor J. Spt4 facilitates the movement of RNA polymerase II through the +2 nucleosomal barrier. Cell Rep 2021; 36:109755. [PMID: 34592154 PMCID: PMC8492961 DOI: 10.1016/j.celrep.2021.109755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/18/2021] [Accepted: 09/02/2021] [Indexed: 02/06/2023] Open
Abstract
Spt4 is a transcription elongation factor with homologs in organisms with nucleosomes. Structural and in vitro studies implicate Spt4 in transcription through nucleosomes, and yet the in vivo function of Spt4 is unclear. Here, we assess the precise position of Spt4 during transcription and the consequences of the loss of Spt4 on RNA polymerase II (RNAPII) dynamics and nucleosome positioning in Saccharomyces cerevisiae. In the absence of Spt4, the spacing between gene-body nucleosomes increases and RNAPII accumulates upstream of the nucleosomal dyad, most dramatically at nucleosome +2. Spt4 associates with elongating RNAPII early in transcription, and its association dynamically changes depending on nucleosome positions. Together, our data show that Spt4 regulates early elongation dynamics, participates in co-transcriptional nucleosome positioning, and promotes RNAPII movement through the gene-body nucleosomes, especially the +2 nucleosome.
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Affiliation(s)
- Ülkü Uzun
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas Brown
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Harry Fischl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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32
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The chromatin remodeler Chd1 supports MRX and Exo1 functions in resection of DNA double-strand breaks. PLoS Genet 2021; 17:e1009807. [PMID: 34520455 PMCID: PMC8462745 DOI: 10.1371/journal.pgen.1009807] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 09/24/2021] [Accepted: 09/06/2021] [Indexed: 12/31/2022] Open
Abstract
Repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) requires that the 5’-terminated DNA strands are resected to generate single-stranded DNA overhangs. This process is initiated by a short-range resection catalyzed by the MRX (Mre11-Rad50-Xrs2) complex, which is followed by a long-range step involving the nucleases Exo1 and Dna2. Here we show that the Saccharomyces cerevisiae ATP-dependent chromatin-remodeling protein Chd1 participates in both short- and long-range resection by promoting MRX and Exo1 association with the DSB ends. Furthermore, Chd1 reduces histone occupancy near the DSB ends and promotes DSB repair by HR. All these functions require Chd1 ATPase activity, supporting a role for Chd1 in the opening of chromatin at the DSB site to facilitate MRX and Exo1 processing activities. DNA double strand breaks (DSBs) are among the most severe types of damage occurring in the genome because their faulty repair can result in chromosome instability, commonly associated with carcinogenesis. Efficient and accurate repair of DSBs relies on several proteins required to process them. However, eukaryotic genomes are compacted into chromatin, which restricts the access to DNA of the enzymes devoted to repair DNA DSBs. To overcome this natural barrier, eukaryotes have evolved chromatin remodeling enzymes that use energy derived from ATP hydrolysis to modulate chromatin structure. Here, we examine the role in DSB repair of the ATP-dependent chromatin remodeler Chd1, which is frequently mutated in prostate cancer. We find that Chd1 is important to repair DNA DSBs by homologous recombination (HR) because it promotes the association with a damaged site of the MRX complex and Exo1, which are necessary to initiate HR. This Chd1 function requires its ATPase activity, suggesting that Chd1 increases the accessibility to chromatin to initiate repair of DNA lesions.
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33
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Banerjee S, Roy S. An insight into understanding the coupling between homologous recombination mediated DNA repair and chromatin remodeling mechanisms in plant genome: an update. Cell Cycle 2021; 20:1760-1784. [PMID: 34437813 DOI: 10.1080/15384101.2021.1966584] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Plants, with their obligatory immobility, are vastly exposed to a wide range of environmental agents and also various endogenous processes, which frequently cause damage to DNA and impose genotoxic stress. These factors subsequently increase genome instability, thus affecting plant growth and productivity. Therefore, to survive under frequent and extreme environmental stress conditions, plants have developed highly efficient and powerful defense mechanisms to repair the damages in the genome for maintaining genome stability. Such multi-dimensional signaling response, activated in presence of damage in the DNA, is collectively known as DNA Damage Response (DDR). DDR plays a crucial role in the remarkably efficient detection, signaling, and repair of damages in the genome for maintaining plant genome stability and normal growth responses. Like other highly advanced eukaryotic systems, chromatin dynamics play a key role in regulating cell cycle progression in plants through remarkable orchestration of environmental and developmental signals. The regulation of chromatin architecture and nucleosomal organization in DDR is mainly modulated by the ATP dependent chromatin remodelers (ACRs), chromatin modifiers, and histone chaperones. ACRs are mainly responsible for transcriptional regulation of several homologous recombination (HR) repair genes in plants under genotoxic stress. The HR-based repair of DNA damage has been considered as the most error-free mechanism of repair and represents one of the essential sources of genetic diversity and new allelic combinations in plants. The initiation of DDR signaling and DNA damage repair pathway requires recruitment of epigenetic modifiers for remodeling of the damaged chromatin while accumulating evidence has shown that chromatin remodeling and DDR share part of the similar signaling pathway through the altered epigenetic status of the associated chromatin region. In this review, we have integrated information to provide an overview on the association between chromatin remodeling mediated regulation of chromatin structure stability and DDR signaling in plants, with emphasis on the scope of the utilization of the available knowledge for the improvement of plant health and productivity.Abbreviation: ADH: Alcohol Dehydrogenase; AGO2: Argonaute 2; ARP: Actin-Related Protein; ASF:1- Anti-Silencing Function-1; ATM: Ataxia Telangiectasia Mutated; ATR: ATM and Rad3- Related; AtSWI3c: Arabidopsis thaliana Switch 3c; ATXR5: Arabidopsis Trithorax-Related5; ATXR6: Arabidopsis Trithorax-Related6; BER: Base Excision Repair; BRCA1: Breast Cancer Associated 1; BRM: BRAHMA; BRU1: BRUSHY1; CAF:1- Chromatin Assembly Factor-1; CHD: Chromodomain Helicase DNA; CHR5: Chromatin Remodeling Protein 5; CHR11/17: Chromatin Remodeling Protein 11/17; CIPK11- CBL- Interacting Protein Kinase 11; CLF: Curly Leaf; CMT3: Chromomethylase 3; COR15A: Cold Regulated 15A; COR47: Cold Regulated 47; CRISPR: Clustered Regulatory Interspaced Short Palindromic Repeats; DDM1: Decreased DNA Methylation1; DRR: DNA Repair and Recombination; DSBs: Double-Strand Breaks; DDR: DNA Damage Response; EXO1: Exonuclease 1; FAS1/2: Fasciata1/2; FACT: Facilitates Chromatin Transcription; FT: Flowering Locus T; GMI1: Gamma-Irradiation And Mitomycin C Induced 1; HAC1: Histone Acetyltransferase of the CBP Family 1; HAM1: Histone Acetyltransferase of the MYST Family 1; HAM2: Histone Acetyltransferase of the MYST Family 2; HAF1: Histone Acetyltransferase of the TAF Family 1; HAT: Histone Acetyl Transferase; HDA1: Histone Deacetylase 1; HDA6: Histone Deacetylase 6; HIRA: Histone Regulatory Homolog A; HR- Homologous recombination; HAS: Helicase SANT Associated; HSS: HAND-SLANT-SLIDE; ICE1: Inducer of CBF Expression 1; INO80: Inositol Requiring Mutant 80; ISW1: Imitation Switch 1; KIN1/2: Kinase 1 /2; MET1: Methyltransferase 1; MET2: Methyltransferase 2; MINU: MINUSCULE; MMS: Methyl Methane Sulfonate; MMS21: Methyl Methane Sulfonate Sensitivity 21; MRN: MRE11, RAD50 and NBS1; MSI1: Multicopy Suppressor Of Ira1; NAP1: Nucleosome Assembly Protein 1; NRP1/NRP2: NAP1-Related Protein; NER: Nucleotide Excision Repair; NHEJ: Non-Homologous End Joining; PARP1: Poly-ADP Ribose Polymerase; PIE1: Photoperiod Independent Early Flowering 1; PIKK: Phosphoinositide 3-Kinase-Like Kinase; PKL: PICKLE; PKR1/2: PICKLE Related 1/2; RAD: Radiation Sensitive Mutant; RD22: Responsive To Desiccation 22; RD29A: Responsive To Desiccation 29A; ROS: Reactive Oxygen Species; ROS1: Repressor of Silencing 1; RPA1E: Replication Protein A 1E; SANT: Swi3, Ada2, N-Cor and TFIIIB; SEP3: SEPALLATA3; SCC3: Sister Chromatid Cohesion Protein 3; SMC1: Structural Maintenance of Chromosomes Protein 1; SMC3: Structural Maintenance of Chromosomes Protein 3; SOG1: Suppressor of Gamma Response 1; SWC6: SWR1 Complex Subunit 6; SWR1: SWI2/SNF2-Related 1; SYD: SPLAYED; SMC5: Structural Maintenance of Chromosome 5; SWI/SNF: Switch/Sucrose Non-Fermentable; TALENs: Transcription Activators Like Effector Nucleases; TRRAP: Transformation/Transactivation Domain-Associated Protein; ZFNs: Zinc Finger Nucleases.
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Affiliation(s)
- Samrat Banerjee
- Department of Botany, UGC Centre for Advanced Studies, the University of Burdwan, Golapbag Campus, Burdwan, West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Centre for Advanced Studies, the University of Burdwan, Golapbag Campus, Burdwan, West Bengal, India
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Sahu RK, Singh S, Tomar RS. The ATP-dependent SWI/SNF and RSC chromatin remodelers cooperatively induce unfolded protein response genes during endoplasmic reticulum stress. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194748. [PMID: 34454103 DOI: 10.1016/j.bbagrm.2021.194748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/01/2021] [Accepted: 08/17/2021] [Indexed: 01/23/2023]
Abstract
The SWI/SNF subfamily remodelers (SWI/SNF and RSC) generally promote gene expression by displacing or evicting nucleosomes at the promoter regions. Their action creates a nucleosome-depleted region where transcription machinery accesses the DNA. Their function has been shown critical for inducing stress-responsive transcription programs. Although the role of SWI/SNF and RSC complexes in transcription regulation of heat shock responsive genes is well studied, their involvement in other pathways such as unfolded protein response (UPR) and protein quality control (PQC) is less known. This study shows that SWI/SNF occupies the promoters of UPR, HSP and PQC genes in response to unfolded protein stress, and its recruitment at UPR promoters depends on Hac1 transcription factor and other epigenetic factors like Ada2 and Ume6. Disruption of SWI/SNF's activity does not affect the remodeling of these promoters or gene expression. However, inactivation of RSC and SWI/SNF together diminishes induction of most of the UPR, HSP and PQC genes tested. Furthermore, RSC and SWI/SNF colocalize at these promoters, suggesting that these two remodelers functionally cooperate to induce stress-responsive genes under proteotoxic conditions.
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Affiliation(s)
- Rakesh Kumar Sahu
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Sakshi Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India.
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Autoinhibitory elements of the Chd1 remodeler block initiation of twist defects by destabilizing the ATPase motor on the nucleosome. Proc Natl Acad Sci U S A 2021; 118:2014498118. [PMID: 33468676 DOI: 10.1073/pnas.2014498118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin remodelers are ATP (adenosine triphosphate)-powered motors that reposition nucleosomes throughout eukaryotic chromosomes. Remodelers possess autoinhibitory elements that control the direction of nucleosome sliding, but underlying mechanisms of inhibition have been unclear. Here, we show that autoinhibitory elements of the yeast Chd1 remodeler block nucleosome sliding by preventing initiation of twist defects. We show that two autoinhibitory elements-the chromodomains and bridge-reinforce each other to block sliding when the DNA-binding domain is not bound to entry-side DNA. Our data support a model where the chromodomains and bridge target nucleotide-free and ADP-bound states of the ATPase motor, favoring a partially disengaged state of the ATPase motor on the nucleosome. By bypassing distortions of nucleosomal DNA prior to ATP binding, we propose that autoinhibitory elements uncouple the ATP binding/hydrolysis cycle from DNA translocation around the histone core.
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Oberbeckmann E, Niebauer V, Watanabe S, Farnung L, Moldt M, Schmid A, Cramer P, Peterson CL, Eustermann S, Hopfner KP, Korber P. Ruler elements in chromatin remodelers set nucleosome array spacing and phasing. Nat Commun 2021; 12:3232. [PMID: 34050140 PMCID: PMC8163753 DOI: 10.1038/s41467-021-23015-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 03/13/2021] [Indexed: 01/09/2023] Open
Abstract
Arrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the 'ruler' that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.
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Affiliation(s)
- Elisa Oberbeckmann
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vanessa Niebauer
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shinya Watanabe
- Program of Molecular Medicine, University of Massachusetts, Worcester, MA, USA
| | - Lucas Farnung
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Manuela Moldt
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrea Schmid
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts, Worcester, MA, USA
| | - Sebastian Eustermann
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.
| | - Karl-Peter Hopfner
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Philipp Korber
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany.
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Genome information processing by the INO80 chromatin remodeler positions nucleosomes. Nat Commun 2021; 12:3231. [PMID: 34050142 PMCID: PMC8163841 DOI: 10.1038/s41467-021-23016-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 04/07/2021] [Indexed: 11/26/2022] Open
Abstract
The fundamental molecular determinants by which ATP-dependent chromatin remodelers organize nucleosomes across eukaryotic genomes remain largely elusive. Here, chromatin reconstitutions on physiological, whole-genome templates reveal how remodelers read and translate genomic information into nucleosome positions. Using the yeast genome and the multi-subunit INO80 remodeler as a paradigm, we identify DNA shape/mechanics encoded signature motifs as sufficient for nucleosome positioning and distinct from known DNA sequence preferences of histones. INO80 processes such information through an allosteric interplay between its core- and Arp8-modules that probes mechanical properties of nucleosomal and linker DNA. At promoters, INO80 integrates this readout of DNA shape/mechanics with a readout of co-evolved sequence motifs via interaction with general regulatory factors bound to these motifs. Our findings establish a molecular mechanism for robust and yet adjustable +1 nucleosome positioning and, more generally, remodelers as information processing hubs that enable active organization and allosteric regulation of the first level of chromatin. DNA sequence preferences or statistical positioning of histones has not explained genomic patterns of nucleosome organisation in vivo. Here, the authors establish DNA shape/mechanics as key elements that have evolved together with binding sites of DNA sequence-specific barriers so that such information directs nucleosome positioning by chromatin remodelers.
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38
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The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution. Sci Rep 2021; 11:4195. [PMID: 33602956 PMCID: PMC7892562 DOI: 10.1038/s41598-021-82842-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
Isw1 and Chd1 are ATP-dependent nucleosome-spacing enzymes required to establish regular arrays of phased nucleosomes near transcription start sites of yeast genes. Cells lacking both Isw1 and Chd1 have extremely disrupted chromatin, with weak phasing, irregular spacing and a propensity to form close-packed dinucleosomes. The Isw1 ATPase subunit occurs in two different remodeling complexes: ISW1a (composed of Isw1 and Ioc3) and ISW1b (composed of Isw1, Ioc2 and Ioc4). The Ioc4 subunit of ISW1b binds preferentially to the H3-K36me3 mark. Here we show that ISW1b is primarily responsible for setting nucleosome spacing and resolving close-packed dinucleosomes, whereas ISW1a plays only a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution, such that neither enzyme is capable of resolving all dinucleosomes on its own. Loss of the Set2 H3-K36 methyltransferase partly phenocopies loss of Ioc4, resulting in increased dinucleosome levels with only a weak effect on nucleosome spacing, suggesting that Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation. The H4 tail domain is required for normal nucleosome spacing but not for dinucleosome resolution. We conclude that the nucleosome spacing and dinucleosome resolving activities of ISW1b and Chd1 are critical for normal global chromatin organisation.
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39
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Donovan DA, Crandall JG, Truong VN, Vaaler AL, Bailey TB, Dinwiddie D, Banks OGB, McKnight LE, McKnight JN. Basis of specificity for a conserved and promiscuous chromatin remodeling protein. eLife 2021; 10:e64061. [PMID: 33576335 PMCID: PMC7968928 DOI: 10.7554/elife.64061] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic genomes are organized dynamically through the repositioning of nucleosomes. Isw2 is an enzyme that has been previously defined as a genome-wide, nonspecific nucleosome spacing factor. Here, we show that Isw2 instead acts as an obligately targeted nucleosome remodeler in vivo through physical interactions with sequence-specific factors. We demonstrate that Isw2-recruiting factors use small and previously uncharacterized epitopes, which direct Isw2 activity through highly conserved acidic residues in the Isw2 accessory protein Itc1. This interaction orients Isw2 on target nucleosomes, allowing for precise nucleosome positioning at targeted loci. Finally, we show that these critical acidic residues have been lost in the Drosophila lineage, potentially explaining the inconsistently characterized function of Isw2-like proteins. Altogether, these data suggest an 'interacting barrier model,' where Isw2 interacts with a sequence-specific factor to accurately and reproducibly position a single, targeted nucleosome to define the precise border of phased chromatin arrays.
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Affiliation(s)
- Drake A Donovan
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | | | - Vi N Truong
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Abigail L Vaaler
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Thomas B Bailey
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Devin Dinwiddie
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Orion GB Banks
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Laura E McKnight
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Jeffrey N McKnight
- Institute of Molecular Biology, University of OregonEugeneUnited States
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugeneUnited States
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40
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Nucleosome Positioning and Spacing: From Mechanism to Function. J Mol Biol 2021; 433:166847. [PMID: 33539878 DOI: 10.1016/j.jmb.2021.166847] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023]
Abstract
Eukaryotes associate their genomes with histone proteins, forming nucleosome particles. Nucleosomes regulate and protect the genetic information. They often assemble into evenly spaced arrays of nucleosomes. These regular nucleosome arrays cover significant portions of the genome, in particular over genes. The presence of these evenly spaced nucleosome arrays is highly conserved throughout the entire eukaryotic domain. Here, we review the mechanisms behind the establishment of this primary structure of chromatin with special emphasis on the biogenesis of evenly spaced nucleosome arrays. We highlight the roles that transcription, nucleosome remodelers, DNA sequence, and histone density play towards the formation of evenly spaced nucleosome arrays and summarize our current understanding of their cellular functions. We end with key unanswered questions that remain to be explored to obtain an in-depth understanding of the biogenesis and function of the nucleosome landscape.
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41
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Qiu H, Biernat E, Govind CK, Rawal Y, Chereji RV, Clark DJ, Hinnebusch AG. Chromatin remodeler Ino80C acts independently of H2A.Z to evict promoter nucleosomes and stimulate transcription of highly expressed genes in yeast. Nucleic Acids Res 2020; 48:8408-8430. [PMID: 32663283 DOI: 10.1093/nar/gkaa571] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/19/2020] [Accepted: 06/29/2020] [Indexed: 12/22/2022] Open
Abstract
The chromatin remodelers SWI/SNF and RSC function in evicting promoter nucleosomes at highly expressed yeast genes, particularly those activated by transcription factor Gcn4. Ino80 remodeling complex (Ino80C) can establish nucleosome-depleted regions (NDRs) in reconstituted chromatin, and was implicated in removing histone variant H2A.Z from the -1 and +1 nucleosomes flanking NDRs; however, Ino80C's function in transcriptional activation in vivo is not well understood. Analyzing the cohort of Gcn4-induced genes in ino80Δ mutants has uncovered a role for Ino80C on par with SWI/SNF in evicting promoter nucleosomes and transcriptional activation. Compared to SWI/SNF, Ino80C generally functions over a wider region, spanning the -1 and +1 nucleosomes, NDR and proximal genic nucleosomes, at genes highly dependent on its function. Defects in nucleosome eviction in ino80Δ cells are frequently accompanied by reduced promoter occupancies of TBP, and diminished transcription; and Ino80 is enriched at genes requiring its remodeler activity. Importantly, nuclear depletion of Ino80 impairs promoter nucleosome eviction even in a mutant lacking H2A.Z. Thus, Ino80C acts widely in the yeast genome together with RSC and SWI/SNF in evicting promoter nucleosomes and enhancing transcription, all in a manner at least partly independent of H2A.Z editing.
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Affiliation(s)
- Hongfang Qiu
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Biernat
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Chhabi K Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Yashpal Rawal
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Reca S, Galello F, Ojeda L, Pautasso C, Cañonero L, Moreno S, Portela P, Rossi S. Chromatin remodeling and transcription of the TPK1 subunit of PKA during stress in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194599. [DOI: 10.1016/j.bbagrm.2020.194599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 01/10/2023]
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43
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Patty BJ, Hainer SJ. Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship. BIOLOGY 2020; 9:E213. [PMID: 32784701 PMCID: PMC7465399 DOI: 10.3390/biology9080213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
Abstract
Eukaryotic genomes are pervasively transcribed, producing both coding and non-coding RNAs (ncRNAs). ncRNAs are diverse and a critical family of biological molecules, yet much remains unknown regarding their functions and mechanisms of regulation. ATP-dependent nucleosome remodeling complexes, in modifying chromatin structure, play an important role in transcriptional regulation. Recent findings show that ncRNAs regulate nucleosome remodeler activities at many levels and that ncRNAs are regulatory targets of nucleosome remodelers. Further, a series of recent screens indicate this network of regulatory interactions is more expansive than previously appreciated. Here, we discuss currently described regulatory interactions between ncRNAs and nucleosome remodelers and contextualize their biological functions.
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Affiliation(s)
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA;
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Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast. BIOLOGY 2020; 9:biology9080190. [PMID: 32722483 PMCID: PMC7466152 DOI: 10.3390/biology9080190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Cellular DNA is packaged into chromatin, which is composed of regularly-spaced nucleosomes with occasional gaps corresponding to active regulatory elements, such as promoters and enhancers, called nucleosome-depleted regions (NDRs). This chromatin organisation is primarily determined by the activities of a set of ATP-dependent remodeling enzymes that are capable of moving nucleosomes along DNA, or of evicting nucleosomes altogether. In yeast, the nucleosome-spacing enzymes are ISW1 (Imitation SWitch protein 1), Chromodomain-Helicase-DNA-binding (CHD)1, ISW2 (Imitation SWitch protein 2) and INOsitol-requiring 80 (INO80); the nucleosome eviction enzymes are the SWItching/Sucrose Non-Fermenting (SWI/SNF) family, the Remodeling the Structure of Chromatin (RSC) complexes and INO80. We discuss the contributions of each set of enzymes to chromatin organisation. ISW1 and CHD1 are the major spacing enzymes; loss of both enzymes results in major chromatin disruption, partly due to the appearance of close-packed di-nucleosomes. ISW1 and CHD1 compete to set nucleosome spacing on most genes. ISW1 is dominant, setting wild type spacing, whereas CHD1 sets short spacing and may dominate on highly-transcribed genes. We propose that the competing remodelers regulate spacing, which in turn controls the binding of linker histone (H1) and therefore the degree of chromatin folding. Thus, genes with long spacing bind more H1, resulting in increased chromatin compaction. RSC, SWI/SNF and INO80 are involved in NDR formation, either directly by nucleosome eviction or repositioning, or indirectly by affecting the size of the complex that resides in the NDR. The nature of this complex is controversial: some suggest that it is a RSC-bound “fragile nucleosome”, whereas we propose that it is a non-histone transcription complex. In either case, this complex appears to serve as a barrier to nucleosome formation, resulting in the formation of phased nucleosomal arrays on both sides.
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Tan LM, Liu R, Gu BW, Zhang CJ, Luo J, Guo J, Wang Y, Chen L, Du X, Li S, Shao CR, Su YN, Cai XW, Lin RN, Li L, Chen S, Du J, He XJ. Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis. THE PLANT CELL 2020; 32:2178-2195. [PMID: 32358072 PMCID: PMC7346560 DOI: 10.1105/tpc.19.00944] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/09/2020] [Accepted: 04/27/2020] [Indexed: 05/07/2023]
Abstract
Chromatin remodeling and histone modifications are important for development and floral transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of Imitation Switch (ISWI) chromatin-remodeling complexes in Arabidopsis (Arabidopsis thaliana). We found that AT-RICH INTERACTING DOMAIN5 (ARID5), a subunit of a plant-specific ISWI complex, can regulate development and floral transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral transition.
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Affiliation(s)
- Lian-Mei Tan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Rui Liu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Bo-Wen Gu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Cui-Jun Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jinyan Luo
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Jing Guo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yuhua Wang
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Lixian Chen
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- National Key Laboratory of Plant Molecular Genetics and Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Du
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Sisi Li
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Chang-Rong Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jiamu Du
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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46
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Lu Y, Tan F, Zhao Y, Zhou S, Chen X, Hu Y, Zhou DX. A Chromodomain-Helicase-DNA-Binding Factor Functions in Chromatin Modification and Gene Regulation. PLANT PHYSIOLOGY 2020; 183:1035-1046. [PMID: 32439720 PMCID: PMC7333708 DOI: 10.1104/pp.20.00453] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/14/2020] [Indexed: 05/07/2023]
Abstract
Proteins in the Chromodomain-Helicase/ATPase-DNA-binding domain (CHD) family are divided into three groups. The function of group I CHD proteins in nucleosome positioning is well established, while that of group II members (represented by CHD3/Mi2) remains unclear. Using high-throughput approaches, we investigated the function of the group II rice (Oryza sativa) CHD protein CHR729 in nucleosome positioning, gene expression, histone methylation, and binding. Our data revealed that the chr729 mutation led to increased nucleosome occupancy in the rice genome and altered the expression and histone H3K4me3 modification of many, mainly underexpressed, genes. Further analysis showed that the mutation affected both the deposition and depletion of H3K4me3 in distinct chromatin regions, with concomitant changes in H3K27me3 modification. Genetic and genomic analyses revealed that CHR729 and JMJ703, an H3K4 demethylase, had agonistic, antagonistic, and independent functions in modulating H3K4me3 and the expression of subsets of genes. In addition, CHR729 binding was enriched in H3K4me3-marked genic and H3K27me3-marked intergenic regions. The results indicate that CHR729 has distinct functions in regulating H3K4me3 and H3K27me3 modifications and gene expression at different chromatin domains and provide insight into chromatin regulation of bivalent genes marked by both H3K4me3 and H3K27me3.
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Affiliation(s)
- Yue Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Feng Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Shaoli Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xiangsong Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yongfeng Hu
- College of Bioengineering, Jingchu University of Technology, 448000 Jingmen, Hubei, China
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, Three Gorges University, 443002 Yichang, Hubei, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
- University Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de Recherche pour L'Agriculture, L'Alimentation et L'Environnement, Institute of Plant Science of Paris-Saclay, 91405 Orsay, France
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47
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Schiessel H, Blossey R. Pioneer transcription factors in chromatin remodeling: The kinetic proofreading view. Phys Rev E 2020; 101:040401. [PMID: 32422793 DOI: 10.1103/physreve.101.040401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Pioneer transcription factors are a recently defined class of transcription factors which can bind directly to nucleosomal DNA; they play a key role in gene activation in certain pathways. Here we quantify their role in the initiation of nucleosome displacement within the kinetic proofreading scenario of chromatin remodeling. The model allows one to perform remodeling efficiency comparisons for scenarios involving different types of transcription factors and remodelers as a function of their binding and unbinding rates and concentrations. Our results demonstrate a way to fine-tune the specificity of processes that modify the chromatin structure in transcriptional initiation.
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Affiliation(s)
- Helmut Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Ralf Blossey
- University of Lille, Unité de Glycobiologie Structurale et Fonctionnelle, CNRS UMR8576, 59000 Lille, France
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48
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Klein-Brill A, Joseph-Strauss D, Appleboim A, Friedman N. Dynamics of Chromatin and Transcription during Transient Depletion of the RSC Chromatin Remodeling Complex. Cell Rep 2020; 26:279-292.e5. [PMID: 30605682 PMCID: PMC6315372 DOI: 10.1016/j.celrep.2018.12.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/19/2018] [Accepted: 12/04/2018] [Indexed: 12/03/2022] Open
Abstract
Nucleosome organization has a key role in transcriptional regulation, yet the precise mechanisms establishing nucleosome locations and their effect on transcription are unclear. Here, we use an induced degradation system to screen all yeast ATP-dependent chromatin remodelers. We characterize how rapid clearance of the remodeler affects nucleosome locations. Specifically, depletion of Sth1, the catalytic subunit of the RSC (remodel the structure of chromatin) complex, leads to rapid fill-in of nucleosome-free regions at gene promoters. These changes are reversible upon reintroduction of Sth1 and do not depend on DNA replication. RSC-dependent nucleosome positioning is pivotal in maintaining promoters of lowly expressed genes free from nucleosomes. In contrast, we observe that upon acute stress, the RSC is not necessary for the transcriptional response. Moreover, RSC-dependent nucleosome positions are tightly related to usage of specific transcription start sites. Our results suggest organizational principles that determine nucleosome positions with and without RSC and how these interact with the transcriptional process. Screen of all yeast ATP-dependent remodelers with a conditional degradation system RSC depletion leads to rapid replication-independent NFR fill-in Recovery of RSC fully reverses NFR fill-in and transcriptional changes RSC-dependent nucleosome positioning directly affect transcription start site choice
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Affiliation(s)
- Avital Klein-Brill
- School of Engineering and Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Daphna Joseph-Strauss
- School of Engineering and Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Alon Appleboim
- School of Engineering and Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Friedman
- School of Engineering and Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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49
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Luo YX, Hou XM, Zhang CJ, Tan LM, Shao CR, Lin RN, Su YN, Cai XW, Li L, Chen S, He XJ. A plant-specific SWR1 chromatin-remodeling complex couples histone H2A.Z deposition with nucleosome sliding. EMBO J 2020; 39:e102008. [PMID: 32115743 DOI: 10.15252/embj.2019102008] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 01/20/2020] [Accepted: 01/28/2020] [Indexed: 01/07/2023] Open
Abstract
Deposition of H2A.Z in chromatin is known to be mediated by a conserved SWR1 chromatin-remodeling complex in eukaryotes. However, little is known about whether and how the SWR1 complex cooperates with other chromatin regulators. Using immunoprecipitation followed by mass spectrometry, we found all known components of the Arabidopsis thaliana SWR1 complex and additionally identified the following three classes of previously uncharacterized plant-specific SWR1 components: MBD9, a methyl-CpG-binding domain-containing protein; CHR11 and CHR17 (CHR11/17), ISWI chromatin remodelers responsible for nucleosome sliding; and TRA1a and TRA1b, accessory subunits of the conserved NuA4 histone acetyltransferase complex. MBD9 directly interacts with CHR11/17 and the SWR1 catalytic subunit PIE1, and is responsible for the association of CHR11/17 with the SWR1 complex. MBD9, TRA1a, and TRA1b function as canonical components of the SWR1 complex to mediate H2A.Z deposition. CHR11/17 are not only responsible for nucleosome sliding but also involved in H2A.Z deposition. These results indicate that the association of the SWR1 complex with CHR11/17 may facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.
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Affiliation(s)
- Yu-Xi Luo
- National Institute of Biological Sciences, Beijing, China
| | - Xiao-Mei Hou
- National Institute of Biological Sciences, Beijing, China
| | - Cui-Jun Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Lian-Mei Tan
- National Institute of Biological Sciences, Beijing, China
| | | | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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50
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Beads on a string-nucleosome array arrangements and folding of the chromatin fiber. Nat Struct Mol Biol 2020; 27:109-118. [PMID: 32042149 DOI: 10.1038/s41594-019-0368-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022]
Abstract
Understanding how the genome is structurally organized as chromatin is essential for understanding its function. Here, we review recent developments that allowed the readdressing of old questions regarding the primary level of chromatin structure, the arrangement of nucleosomes along the DNA and the folding of the nucleosome fiber in nuclear space. In contrast to earlier views of nucleosome arrays as uniformly regular and folded, recent findings reveal heterogeneous array organization and diverse modes of folding. Local structure variations reflect a continuum of functional states characterized by differences in post-translational histone modifications, associated chromatin-interacting proteins and nucleosome-remodeling enzymes.
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