1
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Haase MAB, Lazar-Stefanita L, Ólafsson G, Wudzinska A, Shen MJ, Truong DM, Boeke JD. macroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast. Cell Rep 2024; 43:114472. [PMID: 38990716 DOI: 10.1016/j.celrep.2024.114472] [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: 05/01/2023] [Revised: 01/15/2024] [Accepted: 06/24/2024] [Indexed: 07/13/2024] Open
Abstract
In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones, providing additional layers of structural and epigenetic regulation. Here, we systematically replace individual replicative human histones with non-replicative human variant histones using a histone replacement system in yeast. We show that variants H2A.J, TsH2B, and H3.5 complement their respective replicative counterparts. However, macroH2A1 fails to complement, and its overexpression is toxic in yeast, negatively interacting with yeast's native histones and kinetochore genes. To isolate yeast with macroH2A1 chromatin, we uncouple the effects of its macro and histone fold domains, revealing that both domains suffice to override native nucleosome positioning. Furthermore, both uncoupled constructs of macroH2A1 exhibit lower nucleosome occupancy, decreased short-range chromatin interactions (<20 kb), disrupted centromeric clustering, and increased chromosome instability. Our observations demonstrate that lack of a canonical histone H2A dramatically alters chromatin organization in yeast, leading to genome instability and substantial fitness defects.
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Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY 10016, USA
| | - Luciana Lazar-Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Aleksandra Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Michael J Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - David M Truong
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA; Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA.
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2
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Kumar KK, Aburawi EH, Ljubisavljevic M, Leow MKS, Feng X, Ansari SA, Emerald BS. Exploring histone deacetylases in type 2 diabetes mellitus: pathophysiological insights and therapeutic avenues. Clin Epigenetics 2024; 16:78. [PMID: 38862980 PMCID: PMC11167878 DOI: 10.1186/s13148-024-01692-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Diabetes mellitus is a chronic disease that impairs metabolism, and its prevalence has reached an epidemic proportion globally. Most people affected are with type 2 diabetes mellitus (T2DM), which is caused by a decline in the numbers or functioning of pancreatic endocrine islet cells, specifically the β-cells that release insulin in sufficient quantity to overcome any insulin resistance of the metabolic tissues. Genetic and epigenetic factors have been implicated as the main contributors to the T2DM. Epigenetic modifiers, histone deacetylases (HDACs), are enzymes that remove acetyl groups from histones and play an important role in a variety of molecular processes, including pancreatic cell destiny, insulin release, insulin production, insulin signalling, and glucose metabolism. HDACs also govern other regulatory processes related to diabetes, such as oxidative stress, inflammation, apoptosis, and fibrosis, revealed by network and functional analysis. This review explains the current understanding of the function of HDACs in diabetic pathophysiology, the inhibitory role of various HDAC inhibitors (HDACi), and their functional importance as biomarkers and possible therapeutic targets for T2DM. While their role in T2DM is still emerging, a better understanding of the role of HDACi may be relevant in improving insulin sensitivity, protecting β-cells and reducing T2DM-associated complications, among others.
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Affiliation(s)
- Kukkala Kiran Kumar
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 15551, Al Ain, Abu Dhabi, United Arab Emirates
| | - Elhadi Husein Aburawi
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Milos Ljubisavljevic
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Program, Singapore, Singapore
| | - Melvin Khee Shing Leow
- LKC School of Medicine, Nanyang Technological University, Singapore, Singapore
- Dept of Endocrinology, Tan Tock Seng Hospital, Singapore, Singapore
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Program, Singapore, Singapore
| | - Xu Feng
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Suraiya Anjum Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
- ASPIRE Precision Medicine Research Institute, Abu Dhabi, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 15551, Al Ain, Abu Dhabi, United Arab Emirates.
- Zayed Center for Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates.
- ASPIRE Precision Medicine Research Institute, Abu Dhabi, United Arab Emirates.
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3
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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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4
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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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5
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Yuan T, Yan H, Bailey MLP, Williams JF, Surovtsev I, King MC, Mochrie SGJ. Effect of loops on the mean-square displacement of Rouse-model chromatin. Phys Rev E 2024; 109:044502. [PMID: 38755928 DOI: 10.1103/physreve.109.044502] [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: 04/24/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45-0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010)0031-900710.1103/PhysRevLett.104.238102; Bailey et al., Mol. Biol. Cell 34, ar78 (2023)1059-152410.1091/mbc.E23-04-0119]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static "rosette" loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.
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Affiliation(s)
- Tianyu Yuan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Hao Yan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Jessica F Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Ivan Surovtsev
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Megan C King
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
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6
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Candela-Ferre J, Diego-Martin B, Pérez-Alemany J, Gallego-Bartolomé J. Mind the gap: Epigenetic regulation of chromatin accessibility in plants. PLANT PHYSIOLOGY 2024; 194:1998-2016. [PMID: 38236303 PMCID: PMC10980423 DOI: 10.1093/plphys/kiae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/23/2023] [Indexed: 01/19/2024]
Abstract
Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by limiting access to DNA for various proteins and acting as important signaling hubs. The association of histones with DNA in nucleosomes and the folding of chromatin into higher-order structures are strongly influenced by a variety of epigenetic marks, including DNA methylation, histone variants, and histone post-translational modifications. Additionally, a wide array of chaperones and ATP-dependent remodelers regulate various aspects of nucleosome biology, including assembly, deposition, and positioning. This review provides an overview of recent advances in our mechanistic understanding of how nucleosomes and chromatin organization are regulated by epigenetic marks and remodelers in plants. Furthermore, we present current technologies for profiling chromatin accessibility and organization.
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Affiliation(s)
- Joan Candela-Ferre
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
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7
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Kim JM, Carcamo CC, Jazani S, Xie Z, Feng XA, Yamadi M, Poyton M, Holland KL, Grimm JB, Lavis LD, Ha T, Wu C. Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers. eLife 2024; 12:RP91433. [PMID: 38497611 PMCID: PMC10948146 DOI: 10.7554/elife.91433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement, and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and two-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding, respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/s on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Claudia C Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Sina Jazani
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Zepei Xie
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xinyu A Feng
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Maryam Yamadi
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Matthew Poyton
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Katie L Holland
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of MedicineBaltimoreUnited States
- Howard Hughes Medical InstituteBostonUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins School of MedicineBaltimoreUnited States
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8
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García A, Durán L, Sánchez M, González S, Santamaría R, Antequera F. Asymmetrical nucleosomal DNA signatures regulate transcriptional directionality. Cell Rep 2024; 43:113605. [PMID: 38127622 DOI: 10.1016/j.celrep.2023.113605] [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: 02/16/2023] [Revised: 10/03/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Despite the symmetrical structure of nucleosomes, in vitro studies have shown that transcription proceeds with different efficiency depending on the orientation of the DNA sequence around them. However, it is unclear whether this functional asymmetry is present in vivo and whether it could regulate transcriptional directionality. Here, we report that the proximal and distal halves of nucleosomal DNA contribute differentially to nucleosome stability in the genome. In +1 nucleosomes, this asymmetry facilitates or hinders transcription depending on the orientation of its underlying DNA, and this difference is associated with an asymmetrical interaction between DNA and histones. These properties are encoded in the DNA signature of +1 nucleosomes, since its incorporation in the two orientations into downstream nucleosomes renders them asymmetrically accessible to MNase and inverts the balance between sense and antisense transcription. Altogether, our results show that nucleosomal DNA endows nucleosomes with asymmetrical properties that modulate the directionality of transcription.
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Affiliation(s)
- Alicia García
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Laura Durán
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Sara González
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Rodrigo Santamaría
- Departamento de Informática y Automática, Universidad de Salamanca/Facultad de Ciencias, Plaza de los Caídos s/n, 37007 Salamanca, Spain
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain.
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9
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Kim JM, Carcamo CC, Jazani S, Xie Z, Feng XA, Yamadi M, Poyton M, Holland KL, Grimm JB, Lavis LD, Ha T, Wu C. Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.13.544671. [PMID: 38293098 PMCID: PMC10827135 DOI: 10.1101/2023.06.13.544671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/sec on extended linear DNA under tension. Processivity and opposing push-pull directionalities of nucleosome translocation shown by RSC and ISW2 shape the distinctive landscape of promoter chromatin.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Claudia C. Carcamo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sina Jazani
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zepei Xie
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xinyu A. Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maryam Yamadi
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Poyton
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Katie L. Holland
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
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10
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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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11
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Thenin-Houssier S, Machida S, Jahan C, Bonnet-Madin L, Abbou S, Chen HC, Tesfaye R, Cuvier O, Benkirane M. POLE3 is a repressor of unintegrated HIV-1 DNA required for efficient virus integration and escape from innate immune sensing. SCIENCE ADVANCES 2023; 9:eadh3642. [PMID: 37922361 PMCID: PMC10624344 DOI: 10.1126/sciadv.adh3642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2023]
Abstract
Unintegrated retroviral DNA is transcriptionally silenced by host chromatin silencing factors. Here, we used the proteomics of isolated chromatin segments method to reveal viral and host factors associated with unintegrated HIV-1DNA involved in its silencing. By gene silencing using siRNAs, 46 factors were identified as potential repressors of unintegrated HIV-1DNA. Knockdown and knockout experiments revealed POLE3 as a transcriptional repressor of unintegrated HIV-1DNA. POLE3 maintains unintegrated HIV-1DNA in a repressive chromatin state, preventing RNAPII recruitment to the viral promoter. POLE3 and the recently identified host factors mediating unintegrated HIV-1 DNA silencing, CAF1 and SMC5/SMC6/SLF2, show specificity toward different forms of unintegrated HIV-1DNA. Loss of POLE3 impaired HIV-1 replication, suggesting that repression of unintegrated HIV-1DNA is important for optimal viral replication. POLE3 depletion reduces the integration efficiency of HIV-1. POLE3, by maintaining a repressive chromatin structure of unintegrated HIV-1DNA, ensures HIV-1 escape from innate immune sensing in primary CD4+ T cells.
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Affiliation(s)
- Suzie Thenin-Houssier
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Shinichi Machida
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
- Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Cyprien Jahan
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Lucie Bonnet-Madin
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Scarlette Abbou
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Heng-Chang Chen
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
| | - Robel Tesfaye
- Laboratory of Chromatin Dynamics, Centre de Biologie Intégrative (CBI), MCD Unit (UMR5077), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Olivier Cuvier
- Laboratory of Chromatin Dynamics, Centre de Biologie Intégrative (CBI), MCD Unit (UMR5077), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Monsef Benkirane
- Institut de Génétique Humaine. Laboratoire de Virologie Moléculaire, CNRS Université de Montpellier. Montpellier. France
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12
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Amigo R, Raiqueo F, Tarifeño E, Farkas C, Gutiérrez JL. Poly(dA:dT) Tracts Differentially Modulate Nucleosome Remodeling Activity of RSC and ISW1a Complexes, Exerting Tract Orientation-Dependent and -Independent Effects. Int J Mol Sci 2023; 24:15245. [PMID: 37894925 PMCID: PMC10607297 DOI: 10.3390/ijms242015245] [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: 08/16/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
The establishment and maintenance of nucleosome-free regions (NFRs) are prominent processes within chromatin dynamics. Transcription factors, ATP-dependent chromatin remodeling complexes (CRCs) and DNA sequences are the main factors involved. In Saccharomyces cerevisiae, CRCs such as RSC contribute to chromatin opening at NFRs, while other complexes, including ISW1a, contribute to NFR shrinking. Regarding DNA sequences, growing evidence points to poly(dA:dT) tracts as playing a direct role in active processes involved in nucleosome positioning dynamics. Intriguingly, poly(dA:dT)-tract-containing NFRs span asymmetrically relative to the location of the tract by a currently unknown mechanism. In order to obtain insight into the role of poly(dA:dT) tracts in nucleosome remodeling, we performed a systematic analysis of their influence on the activity of ISW1a and RSC complexes. Our results show that poly(dA:dT) tracts differentially affect the activity of these CRCs. Moreover, we found differences between the effects exerted by the two alternative tract orientations. Remarkably, tract-containing linker DNA is taken as exit DNA for nucleosome sliding catalyzed by RSC. Our findings show that defined DNA sequences, when present in linker DNA, can dictate in which direction a remodeling complex has to slide nucleosomes and shed light into the mechanisms underlying asymmetrical chromatin opening around poly(dA:dT) tracts.
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Affiliation(s)
- Roberto Amigo
- Laboratory of Transcriptional Regulation, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, Concepción 4070043, Chile; (R.A.); (F.R.); (E.T.)
| | - Fernanda Raiqueo
- Laboratory of Transcriptional Regulation, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, Concepción 4070043, Chile; (R.A.); (F.R.); (E.T.)
| | - Estefanía Tarifeño
- Laboratory of Transcriptional Regulation, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, Concepción 4070043, Chile; (R.A.); (F.R.); (E.T.)
| | - Carlos Farkas
- Biomedical Sciences Research Laboratory, Department of Basic Sciences and Morphology, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile;
| | - José L. Gutiérrez
- Laboratory of Transcriptional Regulation, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepción, Concepción 4070043, Chile; (R.A.); (F.R.); (E.T.)
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13
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Abdulhay NJ, Hsieh LJ, McNally CP, Ostrowski MS, Moore CM, Ketavarapu M, Kasinathan S, Nanda AS, Wu K, Chio US, Zhou Z, Goodarzi H, Narlikar GJ, Ramani V. Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. Nat Struct Mol Biol 2023; 30:1571-1581. [PMID: 37696956 PMCID: PMC10584690 DOI: 10.1038/s41594-023-01093-6] [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: 04/24/2023] [Accepted: 08/09/2023] [Indexed: 09/13/2023]
Abstract
Nearly all essential nuclear processes act on DNA packaged into arrays of nucleosomes. However, our understanding of how these processes (for example, DNA replication, RNA transcription, chromatin extrusion and nucleosome remodeling) occur on individual chromatin arrays remains unresolved. Here, to address this deficit, we present SAMOSA-ChAAT: a massively multiplex single-molecule footprinting approach to map the primary structure of individual, reconstituted chromatin templates subject to virtually any chromatin-associated reaction. We apply this method to distinguish between competing models for chromatin remodeling by the essential imitation switch (ISWI) ATPase SNF2h: nucleosome-density-dependent spacing versus fixed-linker-length nucleosome clamping. First, we perform in vivo single-molecule nucleosome footprinting in murine embryonic stem cells, to discover that ISWI-catalyzed nucleosome spacing correlates with the underlying nucleosome density of specific epigenomic domains. To establish causality, we apply SAMOSA-ChAAT to quantify the activities of ISWI ATPase SNF2h and its parent complex ACF on reconstituted nucleosomal arrays of varying nucleosome density, at single-molecule resolution. We demonstrate that ISWI remodelers operate as density-dependent, length-sensing nucleosome sliders, whose ability to program DNA accessibility is dictated by single-molecule nucleosome density. We propose that the long-observed, context-specific regulatory effects of ISWI complexes can be explained in part by the sensing of nucleosome density within epigenomic domains. More generally, our approach promises molecule-precise views of the essential processes that shape nuclear physiology.
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Affiliation(s)
- Nour J Abdulhay
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Laura J Hsieh
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Colin P McNally
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Megan S Ostrowski
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Camille M Moore
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | | | - Sivakanthan Kasinathan
- Department of Pediatrics, Lucille Packard Children's Hospital, Stanford University, Palo Alto, CA, USA
| | - Arjun S Nanda
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Ke Wu
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Un Seng Chio
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Ziling Zhou
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, San Francisco, CA, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
| | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, San Francisco, CA, USA.
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14
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Yadav M, Zuiddam M, Schiessel H. The role of transcript regions and amino acid choice in nucleosome positioning. NAR Genom Bioinform 2023; 5:lqad080. [PMID: 37705829 PMCID: PMC10495542 DOI: 10.1093/nargab/lqad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/19/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
Eukaryotic DNA is organized and compacted in a string of nucleosomes, DNA-wrapped protein cylinders. The positions of nucleosomes along DNA are not random but show well-known base pair sequence preferences that result from the sequence-dependent elastic and geometric properties of the DNA double helix. Here, we focus on DNA around transcription start sites, which are known to typically attract nucleosomes in multicellular life forms through their high GC content. We aim to understand how these GC signals, as observed in genome-wide averages, are produced and encoded through different genomic regions (mainly 5' UTRs, coding exons, and introns). Our study uses a bioinformatics approach to decompose the genome-wide GC signal into between-region and within-region signals. We find large differences in GC signal contributions between vertebrates and plants and, remarkably, even between closely related species. Introns contribute most to the GC signal in vertebrates, while in plants the exons dominate. Further, we find signal strengths stronger on DNA than on mRNA, suggesting a biological function of GC signals along the DNA itself, as is the case for nucleosome positioning. Finally, we make the surprising discovery that both the choice of synonymous codons and amino acids contribute to the nucleosome positioning signal.
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Affiliation(s)
- Manish Yadav
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
| | - Martijn Zuiddam
- Institute Lorentz for Theoretical Physics, Leiden University, Leiden, the Netherlands
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01062 Dresden, Germany
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15
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Haase MAB, Lazar-Stefanita L, Ólafsson G, Wudzinska A, Shen MJ, Truong DM, Boeke JD. Human macroH2A1 drives nucleosome dephasing and genome instability in histone-humanized yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.538725. [PMID: 37205538 PMCID: PMC10187286 DOI: 10.1101/2023.05.06.538725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones providing additional layers of structural and epigenetic regulation. Here, we systematically replaced individual replicative human histones with non-replicative human variant histones using a histone replacement system in yeast. Variants H2A.J, TsH2B, and H3.5 complemented for their respective replicative counterparts. However, macroH2A1 failed to complement and its expression was toxic in yeast, negatively interacting with native yeast histones and kinetochore genes. To isolate yeast with "macroH2A1 chromatin" we decoupled the effects of its macro and histone fold domains, which revealed that both domains sufficed to override native yeast nucleosome positioning. Furthermore, both modified constructs of macroH2A1 exhibited lower nucleosome occupancy that correlated with decreased short-range chromatin interactions (<20 Kb), disrupted centromeric clustering, and increased chromosome instability. While supporting viability, macroH2A1 dramatically alters chromatin organization in yeast, leading to genome instability and massive fitness defects.
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Affiliation(s)
- Max A. B. Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY, 10016, USA
| | - Luciana Lazar-Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Aleksandra Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Michael J. Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - David M. Truong
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
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16
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André KM, Giordanengo Aiach N, Martinez-Fernandez V, Zeitler L, Alberti A, Goldar A, Werner M, Denby Wilkes C, Soutourina J. Functional interplay between Mediator and RSC chromatin remodeling complex controls nucleosome-depleted region maintenance at promoters. Cell Rep 2023; 42:112465. [PMID: 37133993 DOI: 10.1016/j.celrep.2023.112465] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/05/2023] [Accepted: 04/18/2023] [Indexed: 05/04/2023] Open
Abstract
Chromatin organization is crucial for transcriptional regulation in eukaryotes. Mediator is an essential and conserved co-activator thought to act in concert with chromatin regulators. However, it remains largely unknown how their functions are coordinated. Here, we provide evidence in the yeast Saccharomyces cerevisiae that Mediator establishes physical contact with RSC (Remodels the Structure of Chromatin), a conserved and essential chromatin remodeling complex that is crucial for nucleosome-depleted region (NDR) formation. We determine the role of Mediator-RSC interaction in their chromatin binding, nucleosome occupancy, and transcription on a genomic scale. Mediator and RSC co-localize on wide NDRs of promoter regions, and specific Mediator mutations affect nucleosome eviction and TSS-associated +1 nucleosome stability. This work shows that Mediator contributes to RSC remodeling function to shape NDRs and maintain chromatin organization on promoter regions. It will help in our understanding of transcriptional regulation in the chromatin context relevant for severe diseases.
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Affiliation(s)
- Kévin M André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Nathalie Giordanengo Aiach
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Veronica Martinez-Fernandez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Leo Zeitler
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Adriana Alberti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Michel Werner
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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17
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Ovejero-Sánchez M, González-Sarmiento R, Herrero AB. DNA Damage Response Alterations in Ovarian Cancer: From Molecular Mechanisms to Therapeutic Opportunities. Cancers (Basel) 2023; 15:448. [PMID: 36672401 PMCID: PMC9856346 DOI: 10.3390/cancers15020448] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
The DNA damage response (DDR), a set of signaling pathways for DNA damage detection and repair, maintains genomic stability when cells are exposed to endogenous or exogenous DNA-damaging agents. Alterations in these pathways are strongly associated with cancer development, including ovarian cancer (OC), the most lethal gynecologic malignancy. In OC, failures in the DDR have been related not only to the onset but also to progression and chemoresistance. It is known that approximately half of the most frequent subtype, high-grade serous carcinoma (HGSC), exhibit defects in DNA double-strand break (DSB) repair by homologous recombination (HR), and current evidence indicates that probably all HGSCs harbor a defect in at least one DDR pathway. These defects are not restricted to HGSCs; mutations in ARID1A, which are present in 30% of endometrioid OCs and 50% of clear cell (CC) carcinomas, have also been found to confer deficiencies in DNA repair. Moreover, DDR alterations have been described in a variable percentage of the different OC subtypes. Here, we overview the main DNA repair pathways involved in the maintenance of genome stability and their deregulation in OC. We also recapitulate the preclinical and clinical data supporting the potential of targeting the DDR to fight the disease.
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Affiliation(s)
- María Ovejero-Sánchez
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-Spanish National Research Council, 37007 Salamanca, Spain
| | - Rogelio González-Sarmiento
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-Spanish National Research Council, 37007 Salamanca, Spain
| | - Ana Belén Herrero
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-Spanish National Research Council, 37007 Salamanca, Spain
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18
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Muñoz S, Jones A, Bouchoux C, Gilmore T, Patel H, Uhlmann F. Functional crosstalk between the cohesin loader and chromatin remodelers. Nat Commun 2022; 13:7698. [PMID: 36509793 PMCID: PMC9744909 DOI: 10.1038/s41467-022-35444-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
The cohesin complex participates in many structural and functional aspects of genome organization. Cohesin recruitment onto chromosomes requires nucleosome-free DNA and the Scc2-Scc4 cohesin loader complex that catalyzes topological cohesin loading. Additionally, the cohesin loader facilitates promoter nucleosome clearance in a yet unknown way, and it recognizes chromatin receptors such as the RSC chromatin remodeler. Here, we explore the cohesin loader-RSC interaction. Amongst multi-pronged contacts by Scc2 and Scc4, we find that Scc4 contacts a conserved patch on the RSC ATPase motor module. The cohesin loader directly stimulates in vitro nucleosome sliding by RSC, providing an explanation how it facilitates promoter nucleosome clearance. Furthermore, we observe cohesin loader interactions with a wide range of chromatin remodelers. Our results provide mechanistic insight into how the cohesin loader recognizes, as well as influences, the chromatin landscape, with implications for our understanding of human developmental disorders including Cornelia de Lange and Coffin-Siris syndromes.
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Affiliation(s)
- Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
- Cell Cycle Control and the Maintenance of Genomic Stability Laboratory, Cancer Research Center (CIC), University of Salamanca, Salamanca, Spain.
| | - Andrew Jones
- Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Tegan Gilmore
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
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19
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Kadam S, Bameta T, Padinhateeri R. Nucleosome sliding can influence the spreading of histone modifications. Phys Rev E 2022; 106:024408. [PMID: 36110002 DOI: 10.1103/physreve.106.024408] [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: 10/14/2021] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Nucleosomes are the fundamental building blocks of chromatin that not only help in the folding of chromatin, but also in carrying epigenetic information. It is known that nucleosome sliding is responsible for dynamically organizing chromatin structure and the resulting gene regulation. Since sliding can move two neighboring nucleosomes physically close or away, can it play a role in the spreading of histone modifications? We investigate this by simulating a stochastic model that couples nucleosome dynamics with the kinetics of histone modifications. We show that the sliding of nucleosomes can affect the modification pattern as well as the time it takes to modify a given region of chromatin. Exploring different nucleosome densities and modification kinetic parameters, we show that nucleosome sliding can be important for creating histone modification domains. Our model predicts that nucleosome density coupled with sliding dynamics can create an asymmetric histone modification profile around regulatory regions. We also compute the probability distribution of modified nucleosomes and relaxation kinetics of modifications. Our predictions are comparable with known experimental results.
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Affiliation(s)
- Shantanu Kadam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Tripti Bameta
- Department of Medical Oncology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai 410210, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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20
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Heldrich J, Milano CR, Markowitz TE, Ur S, Vale-Silva L, Corbett K, Hochwagen A. Two pathways drive meiotic chromosome axis assembly in Saccharomyces cerevisiae. Nucleic Acids Res 2022; 50:4545-4556. [PMID: 35412621 PMCID: PMC9071447 DOI: 10.1093/nar/gkac227] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 12/16/2022] Open
Abstract
Successful meiotic recombination, and thus fertility, depends on conserved axis proteins that organize chromosomes into arrays of anchored chromatin loops and provide a protected environment for DNA exchange. Here, we show that the stereotypic chromosomal distribution of axis proteins in Saccharomyces cerevisiae is the additive result of two independent pathways: a cohesin-dependent pathway, which was previously identified and mediates focal enrichment of axis proteins at gene ends, and a parallel cohesin-independent pathway that recruits axis proteins to broad genomic islands with high gene density. These islands exhibit elevated markers of crossover recombination as well as increased nucleosome density, which we show is a direct consequence of the underlying DNA sequence. A predicted PHD domain in the center of the axis factor Hop1 specifically mediates cohesin-independent axis recruitment. Intriguingly, other chromosome organizers, including cohesin, condensin, and topoisomerases, are differentially depleted from the same regions even in non-meiotic cells, indicating that these DNA sequence-defined chromatin islands exert a general influence on the patterning of chromosome structure.
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Affiliation(s)
- Jonna Heldrich
- Department of Biology, New York University, New York, NY 10003, USA
| | - Carolyn R Milano
- Department of Biology, New York University, New York, NY 10003, USA
| | | | - Sarah N Ur
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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21
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Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation. Cell Res 2022; 32:801-813. [PMID: 35428874 PMCID: PMC9437020 DOI: 10.1038/s41422-022-00652-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/10/2022] [Indexed: 12/13/2022] Open
Abstract
AbstractChromatin remodeling is essential for epigenome reprogramming after fertilization. However, the underlying mechanisms of chromatin remodeling remain to be explored. Here, we investigated the dynamic changes in nucleosome occupancy and positioning in pronucleus-stage zygotes using ultra low-input MNase-seq. We observed distinct features of inheritance and reconstruction of nucleosome positioning in both paternal and maternal genomes. Genome-wide de novo nucleosome occupancy in the paternal genome was observed as early as 1 h after the injection of sperm into ooplasm. The nucleosome positioning pattern was continually rebuilt to form nucleosome-depleted regions (NDRs) at promoters and transcription factor (TF) binding sites with differential dynamics in paternal and maternal genomes. NDRs formed more quickly on the promoters of genes involved in zygotic genome activation (ZGA), and this formation is closely linked to histone acetylation, but not transcription elongation or DNA replication. Importantly, we found that NDR establishment on the binding motifs of specific TFs might be associated with their potential pioneer functions in ZGA. Further investigations suggested that the predicted factors MLX and RFX1 played important roles in regulating minor and major ZGA, respectively. Our data not only elucidate the nucleosome positioning dynamics in both male and female pronuclei following fertilization, but also provide an efficient method for identifying key transcription regulators during development.
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Lu J, An J, Wang J, Cao X, Cao Y, Huang C, Jiao S, Yan D, Lin X, Zhou X. Znhit1 Regulates p21Cip1 to Control Mouse Lens Differentiation. Invest Ophthalmol Vis Sci 2022; 63:18. [PMID: 35472217 PMCID: PMC9055562 DOI: 10.1167/iovs.63.4.18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/06/2022] [Indexed: 01/22/2023] Open
Abstract
Purpose The transparency of the ocular lens is essential for refracting and focusing light onto the retina, and transparency is controlled by many factors and signaling pathways. Here we showed a critical role of chromatin remodeler zinc finger HIT-type containing 1 (Znhit1) in maintaining lens transparency. Methods To explore the roles of Znhit1 in lens development, the cre-loxp system was used to generate lens-specific Znhit1 knockout mice (Znhit1Mlr10-Cre; Znhit1 cKO). Morphological changes in mice lenses were examined using hematoxylin and eosin staining. RNA sequencing (RNA-seq) and assay for transposase accessible chromatin using sequencing (ATAC-seq) were applied to screen transcriptome changes. Immunofluorescence staining were performed to assess proteins distribution and terminal deoxynucleotidyl transferase dUTP nick-end labeling staining were used for determining apoptosis. The mRNAs expression was examined by quantitative RT-PCR and proteins expression by Western blot. Results Lens-specific conditional knockout mice had a severe cataract, microphthalmia phenotype, and seriously abnormal lens fiber cells differentiation. Deletion of Znhit1 in the lens resulted in decreased cell proliferation and increased cell apoptosis of the lens epithelia. ATAC-seq showed that Znhit1 deficiency increased chromatin accessibility of cyclin-dependent kinase inhibitors, including p57Kip2 and p21Cip1, and upregulated the expression of these genes in mRNA and protein levels. And we also showed that loss of Znhit1 lead to lens fibrosis by upregulating the expression of p21Cip1. Conclusions Our findings suggested that Znhit1 is required for the survival of lens epithelial cells. The loss of Znhit1 leads to the overexpression of p21Cip1, further resulting in lens fibrosis, and impacted the establishment of lens transparency.
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Affiliation(s)
- Juan Lu
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Jianhong An
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Jiawei Wang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Xiaowen Cao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Yuqing Cao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Chengjie Huang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Shiming Jiao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Dongsheng Yan
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiangtian Zhou
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Diseases, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, China
- Research Unit of Myopia Basic Research and Clinical Prevention and Control, Chinese Academy of Medical Sciences, Wenzhou, China
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Abstract
Transcription factors (TFs) are essential mediators of epigenetic regulation and modifiers of penetrance. Studies from the past decades have revealed a sub-class of TF that is capable of remodeling closed chromatin states through targeting nucleosomal motifs. This pioneer factor (PF) class of chromatin remodeler is ATP independent in its roles in epigenetic initiation, with nucleosome-motif recognition and association with repressive chromatin regions. Increasing evidence suggests that the fundamental properties of PFs can be coopted in human cancers. We explore the role of PFs in the larger context of tissue-specific epigenetic regulation. Moreover, we highlight an emerging class of chimeric PF derived from translocation partners in human disease and PFs associated with rare tumors. In the age of site-directed genome editing and targeted protein degradation, increasing our understanding of PFs will provide access to next-generation therapy for human disease driven from altered transcriptional circuitry.
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Kumar A, Zhong Y, Albrecht A, Sang PB, Maples A, Liu Z, Vinayachandran V, Reja R, Lee CF, Kumar A, Chen J, Xiao J, Park B, Shen J, Liu B, Person MD, Trybus KM, Zhang KYJ, Pugh BF, Kamm KE, Milewicz DM, Shen X, Kapoor P. Actin R256 Mono-methylation Is a Conserved Post-translational Modification Involved in Transcription. Cell Rep 2021; 32:108172. [PMID: 32997990 PMCID: PMC8860185 DOI: 10.1016/j.celrep.2020.108172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 07/11/2020] [Accepted: 08/27/2020] [Indexed: 12/19/2022] Open
Abstract
Nuclear actin has been elusive due to the lack of knowledge about molecular mechanisms. From actin-containing chromatin remodeling complexes, we discovered an arginine mono-methylation mark on an evolutionarily conserved R256 residue of actin (R256me1). Actin R256 mutations in yeast affect nuclear functions and cause diseases in human. Interestingly, we show that an antibody specific for actin R256me1 preferentially stains nuclear actin over cytoplasmic actin in yeast, mouse, and human cells. We also show that actin R256me1 is regulated by protein arginine methyl transferase-5 (PRMT5) in HEK293 cells. A genome-wide survey of actin R256me1 mark provides a landscape for nuclear actin correlated with transcription. Further, gene expression and protein interaction studies uncover extensive correlations between actin R256me1 and active transcription. The discovery of actin R256me1 mark suggests a fundamental mechanism to distinguish nuclear actin from cytoplasmic actin through post-translational modification (PTM) and potentially implicates an actin PTM mark in transcription and human diseases. Nuclear actin and actin PTMs are poorly understood. Kumar et al. discover a system of actin PTMs similar to histone PTMs, including a conserved mark on nuclear actin (R256me1) with potential implications for transcription and human diseases.
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Affiliation(s)
- Ashok Kumar
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA
| | - Yuan Zhong
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Amelie Albrecht
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA; The University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Pau Biak Sang
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA
| | - Adrian Maples
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA
| | - Zhenan Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vinesh Vinayachandran
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rohit Reja
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chia-Fang Lee
- ICMB Proteomics Facility, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jiyuan Chen
- Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Jing Xiao
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Bongsoo Park
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Maria D Person
- ICMB Proteomics Facility, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT 05405, USA
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kristine E Kamm
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dianna M Milewicz
- Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Xuetong Shen
- Department of Epigenetics and Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA.
| | - Prabodh Kapoor
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA.
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Barnes T, Korber P. The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo. Int J Mol Sci 2021; 22:ijms22158233. [PMID: 34360997 PMCID: PMC8347975 DOI: 10.3390/ijms22158233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/16/2022] Open
Abstract
Poly(dA:dT) tracts cause nucleosome depletion in many species, e.g., at promoters and replication origins. Their intrinsic biophysical sequence properties make them stiff and unfavorable for nucleosome assembly, as probed by in vitro nucleosome reconstitution. The mere correlation between nucleosome depletion over poly(dA:dT) tracts in in vitro reconstituted and in in vivo chromatin inspired an intrinsic nucleosome exclusion mechanism in vivo that is based only on DNA and histone properties. However, we compile here published and new evidence that this correlation does not reflect mechanistic causation. (1) Nucleosome depletion over poly(dA:dT) in vivo is not universal, e.g., very weak in S. pombe. (2) The energy penalty for incorporating poly(dA:dT) tracts into nucleosomes is modest (<10%) relative to ATP hydrolysis energy abundantly invested by chromatin remodelers. (3) Nucleosome depletion over poly(dA:dT) is much stronger in vivo than in vitro if monitored without MNase and (4) actively maintained in vivo. (5) S. cerevisiae promoters evolved a strand-biased poly(dA) versus poly(dT) distribution. (6) Nucleosome depletion over poly(dA) is directional in vivo. (7) The ATP dependent chromatin remodeler RSC preferentially and directionally displaces nucleosomes towards 5′ of poly(dA). Especially distribution strand bias and displacement directionality would not be expected for an intrinsic mechanism. Together, this argues for an in vivo mechanism where active and species-specific read out of intrinsic sequence properties, e.g., by remodelers, shapes nucleosome organization.
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26
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Kim JM, Visanpattanasin P, Jou V, Liu S, Tang X, Zheng Q, Li KY, Snedeker J, Lavis LD, Lionnet T, Wu C. Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin. eLife 2021; 10:e69387. [PMID: 34313223 PMCID: PMC8352589 DOI: 10.7554/elife.69387] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending 'tug-of-war' that controls a temporally shifting window of accessibility for the transcription initiation machinery.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | | | - Vivian Jou
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Sheng Liu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xiaona Tang
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Kai Yu Li
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Jonathan Snedeker
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Timothee Lionnet
- Institute of Systems Genetics, Langone Medical Center, New York UniversityNew YorkUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins School of MedicineBaltimoreUnited States
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27
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Kumar A, Chan J, Taguchi M, Kono H. Interplay among transacting factors around promoter in the initial phases of transcription. Curr Opin Struct Biol 2021; 71:7-15. [PMID: 34111671 DOI: 10.1016/j.sbi.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
The initiation signals are raised around the promoter by one of the general transcription factors, triggering a sequence of events that lead to mRNA transcript formation from target genes. Both specific noncoding DNA regions and transacting, macromolecular assemblies are intricately involved and indispensable. The transition between the subsequent transcriptional stages is accompanied by stage-specific signals and structural changes in the macromolecular assemblies and facilitated by the recruitment/removal of other chromatin and transcription-associated elements. Here, we discuss the choreography of transacting factors around promoter in the establishment and effectuation of the initial phases of transcription such as NDR formation, +1 nucleosome positioning, promoter DNA opening, and RNAPII promoter escape from a structural viewpoint.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Justin Chan
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Masahiko Taguchi
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.
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28
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Amiad-Pavlov D, Lorber D, Bajpai G, Reuveny A, Roncato F, Alon R, Safran S, Volk T. Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization. SCIENCE ADVANCES 2021; 7:7/23/eabf6251. [PMID: 34078602 PMCID: PMC8172175 DOI: 10.1126/sciadv.abf6251] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 04/15/2021] [Indexed: 05/12/2023]
Abstract
Live imaging of chromatin in an intact organism reveals a novel mode of mesoscale chromatin organization at nuclear periphery.
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Affiliation(s)
- Daria Amiad-Pavlov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dana Lorber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gaurav Bajpai
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Adriana Reuveny
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Roncato
- Department of Immunology Weizmann Institute of Science, Rehovot, Israel
| | - Ronen Alon
- Department of Immunology Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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29
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Barbier J, Vaillant C, Volff JN, Brunet FG, Audit B. Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution. Genes (Basel) 2021; 12:genes12060851. [PMID: 34205881 PMCID: PMC8228248 DOI: 10.3390/genes12060851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics.
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Affiliation(s)
- Jérémy Barbier
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Cédric Vaillant
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
- Correspondence: (J.-N.V.); (B.A.)
| | - Frédéric G. Brunet
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France; (J.B.); (F.G.B.)
| | - Benjamin Audit
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
- Correspondence: (J.-N.V.); (B.A.)
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30
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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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31
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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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32
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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33
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Understanding transcription across scales: From base pairs to chromosomes. Mol Cell 2021; 81:1601-1616. [PMID: 33770487 DOI: 10.1016/j.molcel.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The influence of genome organization on transcription is central to our understanding of cell type specification. Higher-order genome organization is established through short- and long-range DNA interactions. Coordination of these interactions, from single atoms to entire chromosomes, plays a fundamental role in transcriptional control of gene expression. Loss of this coupling can result in disease. Analysis of transcriptional regulation typically involves disparate experimental approaches, from structural studies that define angstrom-level interactions to cell-biological and genomic approaches that assess mesoscale relationships. Thus, to fully understand the mechanisms that regulate gene expression, it is critical to integrate the findings gained across these distinct size scales. In this review, I illustrate fundamental ways in which cells regulate transcription in the context of genome organization.
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34
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Pipkin ME. Runx proteins and transcriptional mechanisms that govern memory CD8 T cell development. Immunol Rev 2021; 300:100-124. [PMID: 33682165 DOI: 10.1111/imr.12954] [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] [Received: 11/06/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
Adaptive immunity to intracellular pathogens and tumors is mediated by antigen-experienced CD8 T cells. Individual naive CD8 T cells have the potential to differentiate into a diverse array of antigen-experienced subsets that exhibit distinct effector functions, life spans, anatomic positioning, and potential for regenerating an entirely new immune response during iterative pathogenic exposures. The developmental process by which activated naive cells undergo diversification involves regulation of chromatin structure and transcription but is not entirely understood. This review examines how alterations in chromatin structure, transcription factor binding, extracellular signals, and single-cell gene expression explain the differential development of distinct effector (TEFF ) and memory (TMEM ) CD8 T cell subsets. Special emphasis is placed on how Runx proteins function with additional transcription factors to pioneer changes in chromatin accessibility and drive transcriptional programs that establish the core attributes of cytotoxic T lymphocytes, subdivide circulating and non-circulating TMEM cell subsets, and govern terminal differentiation. The discussion integrates the roles of specific cytokine signals, transcriptional circuits and how regulation of individual nucleosomes and RNA polymerase II activity can contribute to the process of differentiation. A model that integrates many of these features is discussed to conceptualize how activated CD8 T cells arrive at their fates.
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Affiliation(s)
- Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute - FL, Jupiter, FL, USA
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35
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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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36
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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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37
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Routhier E, Pierre E, Khodabandelou G, Mozziconacci J. Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics. Genome Res 2021; 31:317-326. [PMID: 33355297 PMCID: PMC7849406 DOI: 10.1101/gr.264416.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 12/11/2020] [Indexed: 12/15/2022]
Abstract
Genetically modified genomes are often used today in many areas of fundamental and applied research. In many studies, coding or noncoding regions are modified in order to change protein sequences or gene expression levels. Modifying one or several nucleotides in a genome can also lead to unexpected changes in the epigenetic regulation of genes. When designing a synthetic genome with many mutations, it would thus be very informative to be able to predict the effect of these mutations on chromatin. We develop here a deep learning approach that quantifies the effect of every possible single mutation on nucleosome positions on the full Saccharomyces cerevisiae genome. This type of annotation track can be used when designing a modified S. cerevisiae genome. We further highlight how this track can provide new insights on the sequence-dependent mechanisms that drive nucleosomes' positions in vivo.
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Affiliation(s)
- Etienne Routhier
- Sorbonne Universite, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
| | - Edgard Pierre
- Sorbonne Universite, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
| | | | - Julien Mozziconacci
- Sorbonne Universite, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Paris F-75252, France
- Muséum National d'Histoire Naturelle, Structure et Instabilité des Génomes, UMR7196, Paris 75231, France
- Institut Universitaire de France, Paris 75005, France
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38
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Kharerin H, Bai L. Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast. PLoS Comput Biol 2021; 17:e1008560. [PMID: 33428627 PMCID: PMC7822557 DOI: 10.1371/journal.pcbi.1008560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 01/22/2021] [Accepted: 11/25/2020] [Indexed: 01/09/2023] Open
Abstract
Nucleosome positioning in the genome is essential for the regulation of many nuclear processes. We currently have limited capability to predict nucleosome positioning in vivo, especially the locations and sizes of nucleosome depleted regions (NDRs). Here, we present a thermodynamic model that incorporates the intrinsic affinity of histones, competitive binding of sequence-specific factors, and nucleosome remodeling to predict nucleosome positioning in budding yeast. The model shows that the intrinsic affinity of histones, at near-saturating histone concentration, is not sufficient in generating NDRs in the genome. However, the binding of a few factors, especially RSC towards GC-rich and poly(A/T) sequences, allows us to predict ~ 66% of genome-wide NDRs. The model also shows that nucleosome remodeling activity is required to predict the correct NDR sizes. The validity of the model was further supported by the agreement between the predicted and the measured nucleosome positioning upon factor deletion or on exogenous sequences introduced into yeast. Overall, our model quantitatively evaluated the impact of different genetic components on NDR formation and illustrated the vital roles of sequence-specific factors and nucleosome remodeling in this process. Nucleosome is the basic unit of chromatin, containing 147 base-pairs of DNA wrapped around a histone core. The positioning of nucleosomes, i.e., which parts of DNA are inside nucleosome and which parts are nucleosome-free, is highly regulated. In particular, regulatory sequences tend to be exposed in nucleosome-depleted regions (NDRs), and such exposure is crucial for a variety of processes including DNA replication, repair, and gene expression. Here, we used a thermodynamics model to predict nucleosome positioning on the yeast genome. The model shows that the intrinsic sequence preference of histones is not sufficient in generating NDRs. In contrast, binding of a few transcription factors, especially RSC, is largely responsible for NDR formation. Nucleosome remodeling activity is also required in the model to recapitulate the NDR sizes. This model contributes to our understanding of the mechanisms that regulate nucleosome positioning. It can also be used to predict nucleosome positioning in mutant yeast or on novel DNA sequences.
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Affiliation(s)
- Hungyo Kharerin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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39
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Basu A, Bobrovnikov DG, Qureshi Z, Kayikcioglu T, Ngo TTM, Ranjan A, Eustermann S, Cieza B, Morgan MT, Hejna M, Rube HT, Hopfner KP, Wolberger C, Song JS, Ha T. Measuring DNA mechanics on the genome scale. Nature 2021; 589:462-467. [PMID: 33328628 PMCID: PMC7855230 DOI: 10.1038/s41586-020-03052-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/21/2020] [Indexed: 12/21/2022]
Abstract
Mechanical deformations of DNA such as bending are ubiquitous and have been implicated in diverse cellular functions1. However, the lack of high-throughput tools to measure the mechanical properties of DNA has limited our understanding of how DNA mechanics influence chromatin transactions across the genome. Here we develop 'loop-seq'-a high-throughput assay to measure the propensity for DNA looping-and determine the intrinsic cyclizabilities of 270,806 50-base-pair DNA fragments that span Saccharomyces cerevisiae chromosome V, other genomic regions, and random sequences. We found sequence-encoded regions of unusually low bendability within nucleosome-depleted regions upstream of transcription start sites (TSSs). Low bendability of linker DNA inhibits nucleosome sliding into the linker by the chromatin remodeller INO80, which explains how INO80 can define nucleosome-depleted regions in the absence of other factors2. Chromosome-wide, nucleosomes were characterized by high DNA bendability near dyads and low bendability near linkers. This contrast increases for deeper gene-body nucleosomes but disappears after random substitution of synonymous codons, which suggests that the evolution of codon choice has been influenced by DNA mechanics around gene-body nucleosomes. Furthermore, we show that local DNA mechanics affect transcription through TSS-proximal nucleosomes. Overall, this genome-scale map of DNA mechanics indicates a 'mechanical code' with broad functional implications.
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Affiliation(s)
- Aakash Basu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dmitriy G Bobrovnikov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zan Qureshi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Tunc Kayikcioglu
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Thuy T M Ngo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anand Ranjan
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sebastian Eustermann
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Basilio Cieza
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Michael T Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Miroslav Hejna
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - H Tomas Rube
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karl-Peter Hopfner
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun S Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA.
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40
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He Y, Lawrimore J, Cook D, Van Gorder EE, De Larimat SC, Adalsteinsson D, Forest MG, Bloom K. Statistical mechanics of chromosomes: in vivo and in silico approaches reveal high-level organization and structure arise exclusively through mechanical feedback between loop extruders and chromatin substrate properties. Nucleic Acids Res 2020; 48:11284-11303. [PMID: 33080019 PMCID: PMC7672462 DOI: 10.1093/nar/gkaa871] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/14/2022] Open
Abstract
The revolution in understanding higher order chromosome dynamics and organization derives from treating the chromosome as a chain polymer and adapting appropriate polymer-based physical principles. Using basic principles, such as entropic fluctuations and timescales of relaxation of Rouse polymer chains, one can recapitulate the dominant features of chromatin motion observed in vivo. An emerging challenge is to relate the mechanical properties of chromatin to more nuanced organizational principles such as ubiquitous DNA loops. Toward this goal, we introduce a real-time numerical simulation model of a long chain polymer in the presence of histones and condensin, encoding physical principles of chromosome dynamics with coupled histone and condensin sources of transient loop generation. An exact experimental correlate of the model was obtained through analysis of a model-matching fluorescently labeled circular chromosome in live yeast cells. We show that experimentally observed chromosome compaction and variance in compaction are reproduced only with tandem interactions between histone and condensin, not from either individually. The hierarchical loop structures that emerge upon incorporation of histone and condensin activities significantly impact the dynamic and structural properties of chromatin. Moreover, simulations reveal that tandem condensin–histone activity is responsible for higher order chromosomal structures, including recently observed Z-loops.
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Affiliation(s)
- Yunyan He
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Diana Cook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - David Adalsteinsson
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - M Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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41
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Abstract
Determining whether and how a gene is transcribed are two of the central processes of life. The conceptual basis for understanding such gene regulation arose from pioneering biophysical studies in eubacteria. However, eukaryotic genomes exhibit vastly greater complexity, which raises questions not addressed by this bacterial paradigm. First, how is information integrated from many widely separated binding sites to determine how a gene is transcribed? Second, does the presence of multiple energy-expending mechanisms, which are absent from eubacterial genomes, indicate that eukaryotes are capable of improved forms of genetic information processing? An updated biophysical foundation is needed to answer such questions. We describe the linear framework, a graph-based approach to Markov processes, and show that it can accommodate many previous studies in the field. Under the assumption of thermodynamic equilibrium, we introduce a language of higher-order cooperativities and show how it can rigorously quantify gene regulatory properties suggested by experiment. We point out that fundamental limits to information processing arise at thermodynamic equilibrium and can only be bypassed through energy expenditure. Finally, we outline some of the mathematical challenges that must be overcome to construct an improved biophysical understanding of gene regulation.
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Affiliation(s)
- Felix Wong
- Institute for Medical Engineering & Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA;
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42
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Targeting chromatin dysregulation in organ fibrosis. Cytokine Growth Factor Rev 2020; 57:64-72. [PMID: 32900600 DOI: 10.1016/j.cytogfr.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Fibrosis leads to destruction of organ architecture accompanied by chronic inflammation and loss of function. Fibrosis affects nearly every organ in the body and accounts for ∼45% of total deaths worldwide. Over the past decade, tremendous progress has been made in understanding the basic mechanisms leading to organ fibrosis. However, we are limited with therapeutic options and there is a significant need to develop highly effective anti-fibrotic therapies. Recent advances in sequencing technologies have advanced the burgeoning field of epigenetics towards molecular understanding at a higher resolution. Here we provide a comprehensive review of the recent advances in chromatin regulatory processes, specifically DNA methylation, post-translational modification of histones, and chromatin remodeling complexes in kidney, liver and lung fibrosis. Although this research field is young, we discuss new strategies for potential therapeutic interventions for treating organ fibrosis.
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43
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Jungblut A, Hopfner KP, Eustermann S. Megadalton chromatin remodelers: common principles for versatile functions. Curr Opin Struct Biol 2020; 64:134-144. [PMID: 32771531 DOI: 10.1016/j.sbi.2020.06.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 01/24/2023]
Abstract
ATP-dependent chromatin remodelers are enigmatic macromolecular machines that govern the arrangement and composition of nucleosomes across eukaryotic genomes. Here, we review the recent breakthrough provided by cryo-electron microscopy that reveal the first high-resolution insights into all four families of remodelers. We highlight the emerging structural and mechanistic principles with a particular focus on multi-subunit SWI/SNF and INO80/SWR1 complexes. A conserved architecture comprising a motor, rotor, stator and grip suggests a unifying mechanism for how stepwise DNA translocation enables large scale reconfigurations of nucleosomes. A molecular circuitry involving the nuclear actin containing module establishes a framework for understanding allosteric regulation. Remodelers emerge as programable hubs that enable differential processing of genetic and epigenetic information in response to the physiological state of a cell.
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Affiliation(s)
- Anna Jungblut
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany; Candidate for joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sebastian Eustermann
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.
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44
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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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45
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Ye B, Yang L, Qian G, Liu B, Zhu X, Zhu P, Ma J, Xie W, Li H, Lu T, Wang Y, Wang S, Du Y, Wang Z, Jiang J, Li J, Fan D, Meng S, Wu J, Tian Y, Fan Z. The chromatin remodeler SRCAP promotes self-renewal of intestinal stem cells. EMBO J 2020; 39:e103786. [PMID: 32449550 DOI: 10.15252/embj.2019103786] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
Lgr5+ intestinal stem cells (ISCs) exhibit self-renewal and differentiation features under homeostatic conditions, but the mechanisms controlling Lgr5 + ISC self-renewal remain elusive. Here, we show that the chromatin remodeler SRCAP is highly expressed in mouse intestinal epithelium and ISCs. Srcap deletion impairs both self-renewal of ISCs and intestinal epithelial regeneration. Mechanistically, SRCAP recruits the transcriptional regulator REST to the Prdm16 promoter and induces expression of this transcription factor. By activating PPARδ expression, Prdm16 in turn initiates PPARδ signaling, which sustains ISC stemness. Rest or Prdm16 deficiency abrogates the self-renewal capacity of ISCs as well as intestinal epithelial regeneration. Collectively, these data show that the SRCAP-REST-Prdm16-PPARδ axis is required for self-renewal maintenance of Lgr5 + ISCs.
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Affiliation(s)
- Buqing Ye
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Liuliu Yang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guomin Qian
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Benyu Liu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Pingping Zhu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jing Ma
- MOE Key Laboratory of Bioinformatics, Center for Stem Cell Biology and Regenerative Medicine, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- MOE Key Laboratory of Bioinformatics, Center for Stem Cell Biology and Regenerative Medicine, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huimu Li
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tianku Lu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanying Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shuo Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Du
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhimin Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jing Jiang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Genome Tagging Project (GTP) Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Genome Tagging Project (GTP) Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Dongdong Fan
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shu Meng
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jiayi Wu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yong Tian
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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46
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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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47
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Neipel J, Brandani G, Schiessel H. Translational nucleosome positioning: A computational study. Phys Rev E 2020; 101:022405. [PMID: 32168683 DOI: 10.1103/physreve.101.022405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/25/2019] [Indexed: 01/26/2023]
Abstract
About three-quarters of eukaryotic DNA is wrapped into nucleosomes; DNA spools with a protein core. The affinity of a given DNA stretch to be incorporated into a nucleosome is known to depend on the base-pair sequence-dependent geometry and elasticity of the DNA double helix. This causes the rotational and translational positioning of nucleosomes. In this study we ask the question whether the latter can be predicted by a simple coarse-grained DNA model with sequence-dependent elasticity, the rigid base-pair model. Whereas this model is known to be rather robust in predicting rotational nucleosome positioning, we show that the translational positioning is a rather subtle effect that is dominated by the guanine-cytosine content dependence of entropy rather than energy. A correct qualitative prediction within the rigid base-pair framework can only be achieved by assuming that DNA elasticity effectively changes on complexation into the nucleosome complex. With that extra assumption we arrive at a model which gives an excellent quantitative agreement to experimental in vitro nucleosome maps, under the additional assumption that nucleosomes equilibrate their positions only locally.
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Affiliation(s)
- J Neipel
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Faculty of Physics, Ludwig-Maximilians-Universität München, 80333 München, Germany.,Instituut-Lorentz, Universiteit Leiden, Postbus 9506, 2300 RA Leiden, The Netherlands
| | - G Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - H Schiessel
- Instituut-Lorentz, Universiteit Leiden, Postbus 9506, 2300 RA Leiden, The Netherlands
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48
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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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49
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50
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Duforestel M, Briand J, Bougras-Cartron G, Heymann D, Frenel JS, Vallette FM, Cartron PF. Cell-free circulating epimarks in cancer monitoring. Epigenomics 2020; 12:145-155. [DOI: 10.2217/epi-2019-0170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer numbers increasing, cases heterogeneity and the drug resistance emergence have pushed scientists to search for innovative solutions for patients and epimutations can be one. Methylated DNA, modified nucleosomes and noncoding RNAs are found in all cells, including tumor cells. They are intracellular actors but also have intercellular communication roles, being released in extracellular environment and in different body fluids. Here, we reviewed current literature on the use of these blood circulating epimarks in cancer monitoring. What stands out is that epimarkers must be considered as ‘real time’ images of the tumor, and can be isolated without invasive methods. In the future, the real challenge lies in the development of specific, sensitive, fast and clinically applicable detection and analysis methods of epimarkers.
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Affiliation(s)
- Manon Duforestel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Joséphine Briand
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Gwenola Bougras-Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Dominique Heymann
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
| | - Jean-Sébastien Frenel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- Department of Medical Oncology, Institut de Cancérologie de l'Ouest Site René Gauducheau, Saint Herblain, France
| | - François M Vallette
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
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