1
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Aljahani A, Mauksch C, Oudelaar AM. The relationship between nucleosome positioning and higher-order genome folding. Curr Opin Cell Biol 2024; 89:102398. [PMID: 38991477 DOI: 10.1016/j.ceb.2024.102398] [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: 04/08/2024] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Eukaryotic genomes are organized into 3D structures, which range from small-scale nucleosome arrays to large-scale chromatin domains. These structures have an important role in the regulation of transcription and other nuclear processes. Despite advances in our understanding of the properties, functions, and underlying mechanisms of genome structures, there are many open questions about the interplay between these structures across scales. In particular, it is not well understood if and how 1D features of nucleosome arrays influence large-scale 3D genome folding patterns. In this review, we discuss recent studies that address these questions and summarize our current understanding of the relationship between nucleosome positioning and higher-order genome folding.
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Affiliation(s)
- Abrar Aljahani
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany; University of Göttingen, Göttingen, Germany
| | - Clemens Mauksch
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany; University of Göttingen, Göttingen, Germany
| | - A Marieke Oudelaar
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany.
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2
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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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3
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Wernig-Zorc S, Kugler F, Schmutterer L, Räß P, Hausmann C, Holzinger S, Längst G, Schwartz U. nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome. SCIENCE ADVANCES 2024; 10:eadm9740. [PMID: 38959309 PMCID: PMC11221511 DOI: 10.1126/sciadv.adm9740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Micrococcal nuclease sequencing is the state-of-the-art method for determining chromatin structure and nucleosome positioning. Data analysis is complex due to the AT-dependent sequence bias of the endonuclease and the requirement for high sequencing depth. Here, we present the nucleosome-based MNase accessibility (nucMACC) pipeline unveiling the regulatory chromatin landscape by measuring nucleosome accessibility and stability. The nucMACC pipeline represents a systematic and genome-wide approach for detecting unstable ("fragile") nucleosomes. We have characterized the regulatory nucleosome landscape in Drosophila melanogaster, Saccharomyces cerevisiae, and mammals. Two functionally distinct sets of promoters were characterized, one associated with an unstable nucleosome and the other being nucleosome depleted. We show that unstable nucleosomes present intermediate states of nucleosome remodeling, preparing inducible genes for transcriptional activation in response to stimuli or stress. The presence of unstable nucleosomes correlates with RNA polymerase II proximal pausing. The nucMACC pipeline offers unparalleled precision and depth in nucleosome research and is a valuable tool for future nucleosome studies.
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Affiliation(s)
- Sara Wernig-Zorc
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Fabian Kugler
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Leo Schmutterer
- NGS Analysis Center Biology and Pre-clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Patrick Räß
- NGS Analysis Center Biology and Pre-clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Clemens Hausmann
- NGS Analysis Center Biology and Pre-clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Simon Holzinger
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Gernot Längst
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Uwe Schwartz
- NGS Analysis Center Biology and Pre-clinical Medicine, University of Regensburg, Regensburg, Germany
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4
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Klempahn S, Schiessel H, Blossey R. Chromatin remodelers: a concise introduction for biophysicists. Biophys Rev 2024; 16:357-363. [PMID: 39099840 PMCID: PMC11296983 DOI: 10.1007/s12551-024-01199-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/16/2024] [Indexed: 08/06/2024] Open
Abstract
Chromatin remodelers are molecular motors that act on nucleosomes: they move them along DNA or (dis-)assemble them. Despite the fact that they perform essential regulatory functions in cells-their deregulation can contribute to the development of cancers and lead to cell death-chromatin remodelers have only received meager attention in the biophysics community so far. In this short text, we attempt to present the key features of this interesting class of enzymes obtained with different experimental and theoretical methods, thereby providing a concise introduction for biophysicists to further stimulate interest in their properties.
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Affiliation(s)
- Sophie Klempahn
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, 01307 Dresden, Germany
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, 01307 Dresden, Germany
- Institut für Theoretische Physik, TUD Dresden University of Technology, 01069 Dresden, Germany
| | - Ralf Blossey
- University of Lille, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), CNRS UMR8576, 59000 Lille, France
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5
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Segura J, Díaz-Ingelmo O, Martínez-García B, Ayats-Fraile A, Nikolaou C, Roca J. Nucleosomal DNA has topological memory. Nat Commun 2024; 15:4526. [PMID: 38806488 PMCID: PMC11133463 DOI: 10.1038/s41467-024-49023-4] [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: 06/22/2023] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
One elusive aspect of the chromosome architecture is how it constrains the DNA topology. Nucleosomes stabilise negative DNA supercoils by restraining a DNA linking number difference (∆Lk) of about -1.26. However, whether this capacity is uniform across the genome is unknown. Here, we calculate the ∆Lk restrained by over 4000 nucleosomes in yeast cells. To achieve this, we insert each nucleosome in a circular minichromosome and perform Topo-seq, a high-throughput procedure to inspect the topology of circular DNA libraries in one gel electrophoresis. We show that nucleosomes inherently restrain distinct ∆Lk values depending on their genomic origin. Nucleosome DNA topologies differ at gene bodies (∆Lk = -1.29), intergenic regions (∆Lk = -1.23), rDNA genes (∆Lk = -1.24) and telomeric regions (∆Lk = -1.07). Nucleosomes near the transcription start and termination sites also exhibit singular DNA topologies. Our findings demonstrate that nucleosome DNA topology is imprinted by its native chromatin context and persists when the nucleosome is relocated.
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Affiliation(s)
- Joana Segura
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC/UAM), Madrid, Spain
| | - Ofelia Díaz-Ingelmo
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Belén Martínez-García
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Alba Ayats-Fraile
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | | | - Joaquim Roca
- DNA Topology Lab, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain.
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6
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Garcia J, Paul S, Shukla S, Zhong Y, Beauchemin K, Bartholomew B. Conformational switching of Arp5 subunit differentially regulates INO80 chromatin remodeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593625. [PMID: 38766108 PMCID: PMC11100795 DOI: 10.1101/2024.05.10.593625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The INO80 chromatin remodeler is a versatile enzyme capable of several functions, including spacing nucleosomes equal distances apart, precise positioning of nucleosomes based on DNA shape/sequence and exchanging histone dimers. Within INO80, the Arp5 subunit plays a central role in INO80 remodeling, evidenced by its interactions with the histone octamer, nucleosomal and extranucleosomal DNA, and its necessity in linking INO80's ATPase activity to nucleosome movement. Our investigation reveals that the grappler domain of Arp5 interacts with the acidic pocket of nucleosomes through two distinct mechanisms: an arginine anchor or a hydrophobic/acidic patch. These two modes of binding serve distinct functions within INO80 as shown in vivo by mutations in these regions resulting in varying phenotypes and in vitro by diverse effects on nucleosome mobilization. Our findings suggest that the hydrophobic/acidic patch of Arp5 is likely important for dimer exchange by INO80, while the arginine anchor is crucial for mobilizing nucleosomes.
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Affiliation(s)
- Jeison Garcia
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
- Department of Internal Medicine, Division of Medical Genetics. McGovern Medical School, UT Health Science Center at Houston, TX 77030
- These authors contributed equally
| | - Somnath Paul
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
- These authors contributed equally
| | - Shagun Shukla
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
- These authors contributed equally
| | - Yuan Zhong
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
| | - Karissa Beauchemin
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
- Department of Biology, Texas A&M University, College Station, TX 77843-3474
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77054
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7
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Oyarzún-Cisterna A, Gidi C, Raiqueo F, Amigo R, Rivas C, Torrejón M, Gutiérrez JL. General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex. Biol Res 2024; 57:22. [PMID: 38704609 PMCID: PMC11069190 DOI: 10.1186/s40659-024-00500-6] [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: 01/28/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Chromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors involved in chromatin dynamics at gene regulatory regions are general regulatory factors (GRFs). These factors contribute to establishment and maintenance of nucleosome-depleted regions (NDRs). These regions are populated by nucleosomes through histone deposition and nucleosome sliding, the latter catalyzed by a number of ATP-dependent chromatin remodeling complexes, including ISW1a. It has been observed that GRFs can act as barriers against nucleosome sliding towards NDRs. However, the relative ability of the different GRFs to hinder sliding activity is currently unknown. RESULTS Considering this, we performed a comparative analysis for the main GRFs, with focus in their ability to modulate nucleosome sliding mediated by ISW1a. Among the GRFs tested in nucleosome remodeling assays, Rap1 was the only factor displaying the ability to hinder the activity of ISW1a. This effect requires location of the Rap1 cognate sequence on linker that becomes entry DNA in the nucleosome remodeling process. In addition, Rap1 was able to hinder nucleosome assembly in octamer transfer assays. Concurrently, Rap1 displayed the highest affinity for and longest dwell time from its target sequence, compared to the other GRFs tested. Consistently, through bioinformatics analyses of publicly available genome-wide data, we found that nucleosome occupancy and histone deposition in vivo are inversely correlated with the affinity of Rap1 for its target sequences in the genome. CONCLUSIONS Our findings point to DNA binding affinity, residence time and location at particular translational positions relative to the nucleosome core as the key features of GRFs underlying their roles played in nucleosome sliding and assembly.
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Affiliation(s)
- Andrea Oyarzún-Cisterna
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, 4070043, Concepción, Chile
| | - Cristián Gidi
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, 4070043, Concepción, Chile
| | - Fernanda Raiqueo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, 4070043, Concepción, Chile
| | - Roberto Amigo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, 4070043, Concepción, Chile
| | - Camila Rivas
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, 4070043, Concepción, Chile
| | - Marcela Torrejón
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, 4070043, Concepción, Chile
| | - José L Gutiérrez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, 4070043, Concepción, Chile.
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8
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Rhodes D. To slide or not to slide: key role of the hexasome in chromatin remodeling revealed. Nat Struct Mol Biol 2024; 31:742-746. [PMID: 38769465 DOI: 10.1038/s41594-024-01278-7] [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: 01/11/2024] [Accepted: 03/14/2024] [Indexed: 05/22/2024]
Abstract
Hexasomes are non-canonical nucleosomes that package DNA with six instead of eight histones. First discovered 40 years ago as a consequence of transcription, two near-atomic-resolution cryo-EM structures of the hexasome in complex with the chromatin remodeler INO80 have now started to unravel its mechanistic impact on the regulatory landscape of chromatin. Loss of one histone H2A-H2B dimer converts inactive nucleosomes into distinct and favorable substrates for ATP-dependent chromatin remodeling.
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Affiliation(s)
- Daniela Rhodes
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK.
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9
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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10
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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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11
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Wu K, Dhillon N, Bajor A, Abrahamsson S, Kamakaka RT. Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration. Cell Rep 2024; 43:113983. [PMID: 38517895 PMCID: PMC11141299 DOI: 10.1016/j.celrep.2024.113983] [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: 08/24/2023] [Revised: 12/25/2023] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae involves the generation of a chromatin state that stably represses transcription. Using multiple reporter assays, a diverse set of upstream activating sequence enhancers and core promoters were investigated for their susceptibility to silencing. We show that heterochromatin stably silences only weak and stress-induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements, and the partial repression of these elements did not result in bistable expression states. Permutation analysis of enhancers and promoters indicates that both elements are targets of repression. Chromatin remodelers help specific regulatory elements to resist repression, most probably by altering nucleosome mobility and changing transcription burst duration. The strong enhancers/promoters can be repressed if silencer-bound Sir1 is increased. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating-type gene regulatory elements but not strong housekeeping gene regulatory sequences.
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Affiliation(s)
- Kenneth Wu
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Namrita Dhillon
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Antone Bajor
- Electrical Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Sara Abrahamsson
- Electrical Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Rohinton T Kamakaka
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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12
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Xi S, Nguyen T, Murray S, Lorenz P, Mellor J. Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes. Yeast 2024; 41:222-241. [PMID: 38433440 DOI: 10.1002/yea.3931] [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: 10/30/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Genomes from yeast to humans are subject to pervasive transcription. A single round of pervasive transcription is sufficient to alter local chromatin conformation, nucleosome dynamics and gene expression, but is hard to distinguish from background signals. Size fractionated native elongating transcript sequencing (sfNET-Seq) was developed to precisely map nascent transcripts independent of expression levels. RNAPII-associated nascent transcripts are fractionation into different size ranges before library construction. When anchored to the transcription start sites (TSS) of annotated genes, the combined pattern of the output metagenes gives the expected reference pattern. Bioinformatic pattern matching to the reference pattern identified 9542 transcription units in Saccharomyces cerevisiae, of which 47% are coding and 53% are noncoding. In total, 3113 (33%) are unannotated noncoding transcription units. Anchoring all transcription units to the TSS or polyadenylation site (PAS) of annotated genes reveals distinctive architectures of linked pairs of divergent transcripts approximately 200nt apart. The Reb1 transcription factor is enriched 30nt downstream of the PAS only when an upstream (TSS -60nt with respect to PAS) noncoding transcription unit co-occurs with a downstream (TSS +150nt) coding transcription unit and acts to limit levels of upstream antisense transcripts. The potential for extensive transcriptional interference is evident from low abundance unannotated transcription units with variable TSS (median -240nt) initiating within a 500nt window upstream of, and transcribing over, the promoters of protein-coding genes. This study confirms a highly interleaved yeast genome with different types of transcription units altering the chromatin landscape in distinctive ways, with the potential to exert extensive regulatory control.
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Affiliation(s)
- Shidong Xi
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Tania Nguyen
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Struan Murray
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Phil Lorenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
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13
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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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14
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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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15
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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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16
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Oberbeckmann E, Quililan K, Cramer P, Oudelaar AM. In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization. Nat Genet 2024; 56:483-492. [PMID: 38291333 PMCID: PMC10937381 DOI: 10.1038/s41588-023-01649-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 12/15/2023] [Indexed: 02/01/2024]
Abstract
Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms driving the formation of these domains are difficult to dissect in vivo and remain poorly understood. Here we reconstitute Saccharomyces cerevisiae chromatin in vitro and determine its 3D organization at subnucleosome resolution by micrococcal nuclease-based chromosome conformation capture and molecular dynamics simulations. We show that regularly spaced and phased nucleosome arrays form chromatin domains in vitro that resemble domains in vivo. This demonstrates that neither loop extrusion nor transcription is required for basic domain formation in yeast. In addition, we find that the boundaries of reconstituted domains correspond to nucleosome-free regions and that insulation strength scales with their width. Finally, we show that domain compaction depends on nucleosome linker length, with longer linkers forming more compact structures. Together, our results demonstrate that regular nucleosome positioning is important for the formation of chromatin domains and provide a proof-of-principle for bottom-up 3D genome studies.
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Affiliation(s)
- Elisa Oberbeckmann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany.
| | - Kimberly Quililan
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany
- The Francis Crick Institute, London, UK
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Göttingen, Germany
| | - A Marieke Oudelaar
- Max Planck Institute for Multidisciplinary Sciences, Genome Organization and Regulation, Göttingen, Germany.
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17
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Busby T, Misteli T. Building chromatin from the ground up. Nat Genet 2024; 56:360-361. [PMID: 38351384 DOI: 10.1038/s41588-024-01666-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024]
Affiliation(s)
- Theodore Busby
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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18
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Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z. Structure of the ISW1a complex bound to the dinucleosome. Nat Struct Mol Biol 2024; 31:266-274. [PMID: 38177688 DOI: 10.1038/s41594-023-01174-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin organization and gene expression. Here we report the cryo-EM structure of chromatin remodeler ISW1a complex from Saccharomyces cerevisiae bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, while the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a and add a new mode of nucleosome remodeling in the context of a chromatin environment.
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Affiliation(s)
- Lifei Li
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Kangjing Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Youyang Sia
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Pengjing Hu
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Youpi Ye
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China
- School of Life Science, Tsinghua University, Beijing, P.R. China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China
| | - Zhucheng Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China.
- School of Life Science, Tsinghua University, Beijing, P.R. China.
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, P.R. China.
- Beijing Frontier Research Center for Biological Structure, Beijing, P.R. China.
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19
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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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20
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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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21
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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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22
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Zeitler L, André K, Alberti A, Denby Wilkes C, Soutourina J, Goldar A. A genome-wide comprehensive analysis of nucleosome positioning in yeast. PLoS Comput Biol 2024; 20:e1011799. [PMID: 38266035 PMCID: PMC10843174 DOI: 10.1371/journal.pcbi.1011799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 02/05/2024] [Accepted: 01/03/2024] [Indexed: 01/26/2024] Open
Abstract
In eukaryotic cells, the one-dimensional DNA molecules need to be tightly packaged into the spatially constraining nucleus. Folding is achieved on its lowest level by wrapping the DNA around nucleosomes. Their arrangement regulates other nuclear processes, such as transcription and DNA repair. Despite strong efforts to study nucleosome positioning using Next Generation Sequencing (NGS) data, the mechanism of their collective arrangement along the gene body remains poorly understood. Here, we classify nucleosome distributions of protein-coding genes in Saccharomyces cerevisiae according to their profile similarity and analyse their differences using functional Principal Component Analysis. By decomposing the NGS signals into their main descriptive functions, we compared wild type and chromatin remodeler-deficient strains, keeping position-specific details preserved whilst considering the nucleosome arrangement as a whole. A correlation analysis with other genomic properties, such as gene size and length of the upstream Nucleosome Depleted Region (NDR), identified key factors that influence the nucleosome distribution. We reveal that the RSC chromatin remodeler-which is responsible for NDR maintenance-is indispensable for decoupling nucleosome arrangement within the gene from positioning outside, which interfere in rsc8-depleted conditions. Moreover, nucleosome profiles in chd1Δ strains displayed a clear correlation with RNA polymerase II presence, whereas wild type cells did not indicate a noticeable interdependence. We propose that RSC is pivotal for global nucleosome organisation, whilst Chd1 plays a key role for maintaining local arrangement.
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Affiliation(s)
- Leo Zeitler
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Kévin André
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Adriana Alberti
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
| | - Arach Goldar
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC),Gif-sur-Yvette, France
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23
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Converso C, Pierrakeas L, Chan L, Chowdhury S, Kuznetsov VI, Denu JM, Luk E. Nucleic acid sequence contributes to remodeler-mediated targeting of histone H2A.Z. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570360. [PMID: 38106078 PMCID: PMC10723385 DOI: 10.1101/2023.12.06.570360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The variant histone H2A.Z is inserted into nucleosomes immediately downstream of promoters and is important for transcription. The site-specific deposition of H2A.Z is catalyzed by SWR, a conserved chromatin remodeler with affinity for promoter-proximal nucleosome depleted regions (NDRs) and histone acetylation. By comparing the genomic distribution of H2A.Z in wild-type and SWR-deficient cells, we found that SWR is also responsible for depositing H2A.Z at thousands of non-canonical sites not directly linked to NDRs or histone acetylation. To understand the targeting mechanism of H2A.Z, we presented SWR with a library of nucleosomes isolated from yeast and characterized those preferred by SWR. We found that SWR prefers nucleosomes associated with intergenic over coding regions, especially when polyadenine tracks are present. Insertion of polyadenine sequences into recombinant nucleosomes near the H2A-H2B binding site stimulated the H2A.Z insertion activity of SWR. Therefore, the genome is encoded with information contributing to remodeler-mediated targeting of H2A.Z.
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24
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Biswas A, Basu A. The impact of the sequence-dependent physical properties of DNA on chromatin dynamics. Curr Opin Struct Biol 2023; 83:102698. [PMID: 37696706 DOI: 10.1016/j.sbi.2023.102698] [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: 04/17/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023]
Abstract
The local mechanical properties of DNA depend on local sequence. Here we review recent genomic, structural, and computational efforts at deciphering the "mechanical code", i.e., the mapping between sequence and mechanics. We then discuss works that suggest how evolution has exploited the mechanical code to control the energetics of DNA-deforming biological processes such as nucleosome organization, transcription factor binding, DNA supercoiling, gene regulation, and 3D chromatin organization. As a whole, these recent works suggest that DNA sequence in diverse organisms can encode regulatory information governing diverse processes via the mechanical code.
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Affiliation(s)
- Aditi Biswas
- Department of Biosciences, Durham University, Durham, UK
| | - Aakash Basu
- Department of Biosciences, Durham University, Durham, UK.
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25
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Barrasa JI, Kahn TG, Lundkvist MJ, Schwartz YB. DNA elements tether canonical Polycomb Repressive Complex 1 to human genes. Nucleic Acids Res 2023; 51:11613-11633. [PMID: 37855680 PMCID: PMC10681801 DOI: 10.1093/nar/gkad889] [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: 03/08/2023] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Development of multicellular animals requires epigenetic repression by Polycomb group proteins. The latter assemble in multi-subunit complexes, of which two kinds, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2), act together to repress key developmental genes. How PRC1 and PRC2 recognize specific genes remains an open question. Here we report the identification of several hundreds of DNA elements that tether canonical PRC1 to human developmental genes. We use the term tether to describe a process leading to a prominent presence of canonical PRC1 at certain genomic sites, although the complex is unlikely to interact with DNA directly. Detailed analysis indicates that sequence features associated with PRC1 tethering differ from those that favour PRC2 binding. Throughout the genome, the two kinds of sequence features mix in different proportions to yield a gamut of DNA elements that range from those tethering predominantly PRC1 or PRC2 to ones capable of tethering both complexes. The emerging picture is similar to the paradigmatic targeting of Polycomb complexes by Polycomb Response Elements (PREs) of Drosophila but providing for greater plasticity.
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Affiliation(s)
- Juan I Barrasa
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Tatyana G Kahn
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Moa J Lundkvist
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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26
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Bartholomew B, Shukla S, Ngubo M, Paul S, Persinger J, Brahma S. New insights into the mechanism and DNA-sequence specificity of INO80 chromatin remodeling. RESEARCH SQUARE 2023:rs.3.rs-3443329. [PMID: 37961512 PMCID: PMC10635376 DOI: 10.21203/rs.3.rs-3443329/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The INO80 complex stood out in a large family of ATP-dependent chromatin remodelers because of its ATPase domain binding and translocating on DNA at the edge of nucleosomes, rather than at two helical turns from the center of DNA that is wrapped around nucleosomes. This unique property of INO80 was thought to account for its singular role in nucleosome placement at gene promoters in a DNA-sequence dependent manner that is crucial for transcription regulation. Now, we uncover INO80 functions differently than previously thought with its ATPase domain translocating on DNA close to the center of nucleosomes, like other remodelers. Our discovery also reveals the physical properties of the first ~36 bp of DNA on the entry side of nucleosomes is the main determinant for the DNA specificity of INO80 rather than the properties of the extranucleosomal DNA. The DNA sequence sensitive step of INO80 is after DNA is displaced from the histone octamer on the entry side of nucleosomes and 20 bp of DNA are moved out the exit side. We find the ATPase domain and Arp5 subunit of INO80 are likely involved in INO80's DNA specificity and the mechanism of INO80 remodeling is substantially different than originally proposed.
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27
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Park S, Brandani GB, Ha T, Bowman G. Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning. Nucleic Acids Res 2023; 51:10326-10343. [PMID: 37738162 PMCID: PMC10602870 DOI: 10.1093/nar/gkad738] [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: 03/11/2022] [Revised: 08/02/2023] [Accepted: 08/26/2023] [Indexed: 09/24/2023] Open
Abstract
Chromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone core. Although not directly reading out the DNA sequence, some chromatin remodelers exhibit a sequence-dependent bias in nucleosome positioning, which presumably reflects properties of the DNA duplex. Here, we show how nucleosome positioning by the Chd1 remodeler is influenced by local DNA perturbations throughout the nucleosome footprint. Using site-specific DNA cleavage coupled with next-generation sequencing, we show that nucleosomes shifted by Chd1 can preferentially localize DNA perturbations - poly(dA:dT) tracts, DNA mismatches, and single-nucleotide insertions - about a helical turn outside the Chd1 motor domain binding site, super helix location 2 (SHL2). This phenomenon occurs with both the Widom 601 positioning sequence and the natural +1 nucleosome sequence from the Saccharomyces cerevisiae SWH1 gene. Our modeling indicates that localization of DNA perturbations about a helical turn outward from SHL2 results from back-and-forth sliding due to remodeler action on both sides of the nucleosome. Our results also show that barrier effects from DNA perturbations can be extended by the strong phasing of nucleosome positioning sequences.
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Affiliation(s)
- Sangwoo Park
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Gregory D Bowman
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
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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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29
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Wu K, Dhillon N, Bajor A, Abrahamson S, Kamakaka RT. Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561072. [PMID: 37873261 PMCID: PMC10592971 DOI: 10.1101/2023.10.05.561072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The interplay between nucleosomes and transcription factors leads to programs of gene expression. Transcriptional silencing involves the generation of a chromatin state that represses transcription and is faithfully propagated through DNA replication and cell division. Using multiple reporter assays, including directly visualizing transcription in single cells, we investigated a diverse set of UAS enhancers and core promoters for their susceptibility to heterochromatic gene silencing. These results show that heterochromatin only stably silences weak and stress induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements and the partial repression did not result in bistable expression states. Permutation analysis of different UAS enhancers and core promoters indicate that both elements function together to determine the susceptibility of regulatory sequences to repression. Specific histone modifiers and chromatin remodellers function in an enhancer specific manner to aid these elements to resist repression suggesting that Sir proteins likely function in part by reducing nucleosome mobility. We also show that the strong housekeeping regulatory elements can be repressed if silencer bound Sir1 is increased, suggesting that Sir1 is a limiting component in silencing. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating type gene regulatory elements but not strong housekeeping gene regulatory sequences which could help explain why these genes are often found at the boundaries of silenced domains.
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Affiliation(s)
- Kenneth Wu
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Namrita Dhillon
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Antone Bajor
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Sara Abrahamson
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Rohinton T. Kamakaka
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
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30
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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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31
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Jonas F, Vidavski M, Benuck E, Barkai N, Yaakov G. Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA-protein binding. Nucleic Acids Res 2023; 51:8496-8513. [PMID: 37493599 PMCID: PMC10484674 DOI: 10.1093/nar/gkad615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023] Open
Abstract
DNA packaging within chromatin depends on histone chaperones and remodelers that form and position nucleosomes. Cells express multiple such chromatin regulators with overlapping in-vitro activities. Defining specific in-vivo activities requires monitoring histone dynamics during regulator depletion, which has been technically challenging. We have recently generated histone-exchange sensors in Saccharomyces cerevisiae, which we now use to define the contributions of 15 regulators to histone dynamics genome-wide. While replication-independent exchange in unperturbed cells maps to promoters, regulator depletions primarily affected gene bodies. Depletion of Spt6, Spt16 or Chd1 sharply increased nucleosome replacement sequentially at the beginning, middle or end of highly expressed gene bodies. They further triggered re-localization of chaperones to affected gene body regions, which compensated for nucleosome loss during transcription complex passage, but concurred with extensive TF binding in gene bodies. We provide a unified quantitative screen highlighting regulator roles in retaining nucleosome binding during transcription and preserving genomic packaging.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Matan Vidavski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eli Benuck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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32
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Reese JC. New roles for elongation factors in RNA polymerase II ubiquitylation and degradation. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194956. [PMID: 37331651 PMCID: PMC10527621 DOI: 10.1016/j.bbagrm.2023.194956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
RNA polymerase II (RNAPII) encounters numerous impediments on its way to completing mRNA synthesis across a gene. Paused and arrested RNAPII are reactivated or rescued by elongation factors that travel with polymerase as it transcribes DNA. However, when RNAPII fails to resume transcription, such as when it encounters an unrepairable bulky DNA lesion, it is removed by the targeting of its largest subunit, Rpb1, for degradation by the ubiquitin-proteasome system (UPS). We are starting to understand this process better and how the UPS marks Rbp1 for degradation. This review will focus on the latest developments and describe new functions for elongation factors that were once thought to only promote elongation in unstressed conditions in the removal and degradation of RNAPII. I propose that in addition to changes in RNAPII structure, the composition and modification of elongation factors in the elongation complex determine whether to rescue or degrade RNAPII.
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Affiliation(s)
- Joseph C Reese
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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33
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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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34
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Woodhouse M, Brooks Crickard J. DNA curtains to visualize chromatin interactions. Methods 2023; 217:36-42. [PMID: 37437647 PMCID: PMC10529070 DOI: 10.1016/j.ymeth.2023.07.001] [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: 01/11/2023] [Revised: 05/26/2023] [Accepted: 07/09/2023] [Indexed: 07/14/2023] Open
Abstract
Recent advances in single molecule imaging have allowed the evolution of biochemical techniques that directly visualize protein-DNA interactions in real-time. These techniques rely on diffraction limited total internal reflection microscopy (TIRFM), and have significantly improved our understanding of RNA transcription, DNA replication, homologous recombination, and general DNA repair in the context of chromatin. Here we described a general single molecule TIRFM technique called DNA curtains to directly visualize how enzymes function on chromatinized DNA. The goal of this manuscript is to introduce the reader to methods to express and reconstitute nucleosomes on long stretches of DNA, and to directly visualize this process using DNA curtains with TIRFM.
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Affiliation(s)
- Mitchell Woodhouse
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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35
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Kleinschmidt H, Xu C, Bai L. Using Synthetic DNA Libraries to Investigate Chromatin and Gene Regulation. Chromosoma 2023; 132:167-189. [PMID: 37184694 PMCID: PMC10542970 DOI: 10.1007/s00412-023-00796-5] [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: 02/05/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/16/2023]
Abstract
Despite the recent explosion in genome-wide studies in chromatin and gene regulation, we are still far from extracting a set of genetic rules that can predict the function of the regulatory genome. One major reason for this deficiency is that gene regulation is a multi-layered process that involves an enormous variable space, which cannot be fully explored using native genomes. This problem can be partially solved by introducing synthetic DNA libraries into cells, a method that can test the regulatory roles of thousands to millions of sequences with limited variables. Here, we review recent applications of this method to study transcription factor (TF) binding, nucleosome positioning, and transcriptional activity. We discuss the design principles, experimental procedures, and major findings from these studies and compare the pros and cons of different approaches.
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Affiliation(s)
- Holly Kleinschmidt
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Physics, The Pennsylvania State University, University Park, PA, 16802, USA.
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36
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Zhang M, Jungblut A, Kunert F, Hauptmann L, Hoffmann T, Kolesnikova O, Metzner F, Moldt M, Weis F, DiMaio F, Hopfner KP, Eustermann S. Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling. Science 2023; 381:313-319. [PMID: 37384673 DOI: 10.1126/science.adf6287] [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: 11/03/2022] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Loss of H2A-H2B histone dimers is a hallmark of actively transcribed genes, but how the cellular machinery functions in the context of noncanonical nucleosomal particles remains largely elusive. In this work, we report the structural mechanism for adenosine 5'-triphosphate-dependent chromatin remodeling of hexasomes by the INO80 complex. We show how INO80 recognizes noncanonical DNA and histone features of hexasomes that emerge from the loss of H2A-H2B. A large structural rearrangement switches the catalytic core of INO80 into a distinct, spin-rotated mode of remodeling while its nuclear actin module remains tethered to long stretches of unwrapped linker DNA. Direct sensing of an exposed H3-H4 histone interface activates INO80, independently of the H2A-H2B acidic patch. Our findings reveal how the loss of H2A-H2B grants remodelers access to a different, yet unexplored layer of energy-driven chromatin regulation.
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Affiliation(s)
- Min Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anna Jungblut
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Franziska Kunert
- Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Luis Hauptmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thomas Hoffmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Olga Kolesnikova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Felix Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Manuela Moldt
- Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Felix Weis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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37
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Gvozdenov Z, Barcutean Z, Struhl K. Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells. Mol Cell 2023; 83:1786-1797.e5. [PMID: 37137302 PMCID: PMC10247422 DOI: 10.1016/j.molcel.2023.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/18/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
We measure transcriptional noise in yeast by analyzing chromatin structure and transcription of an 18-kb region of DNA whose sequence was randomly generated. Nucleosomes fully occupy random-sequence DNA, but nucleosome-depleted regions (NDRs) are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays. Steady-state levels of random-sequence RNAs are comparable to yeast mRNAs, although transcription and decay rates are higher. Transcriptional initiation from random-sequence DNA occurs at numerous sites, indicating very low intrinsic specificity of the RNA Pol II machinery. In contrast, poly(A) profiles of random-sequence RNAs are roughly comparable to those of yeast mRNAs, suggesting limited evolutionary restraints on poly(A) site choice. Random-sequence RNAs show higher cell-to-cell variability than yeast mRNAs, suggesting that functional elements limit variability. These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.
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Affiliation(s)
- Zlata Gvozdenov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zeno Barcutean
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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38
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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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39
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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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40
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Chacin E, Reusswig KU, Furtmeier J, Bansal P, Karl LA, Pfander B, Straub T, Korber P, Kurat CF. Establishment and function of chromatin organization at replication origins. Nature 2023; 616:836-842. [PMID: 37020028 DOI: 10.1038/s41586-023-05926-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/03/2023] [Indexed: 04/07/2023]
Abstract
The origin recognition complex (ORC) is essential for initiation of eukaryotic chromosome replication as it loads the replicative helicase-the minichromosome maintenance (MCM) complex-at replication origins1. Replication origins display a stereotypic nucleosome organization with nucleosome depletion at ORC-binding sites and flanking arrays of regularly spaced nucleosomes2-4. However, how this nucleosome organization is established and whether this organization is required for replication remain unknown. Here, using genome-scale biochemical reconstitution with approximately 300 replication origins, we screened 17 purified chromatin factors from budding yeast and found that the ORC established nucleosome depletion over replication origins and flanking nucleosome arrays by orchestrating the chromatin remodellers INO80, ISW1a, ISW2 and Chd1. The functional importance of the nucleosome-organizing activity of the ORC was demonstrated by orc1 mutations that maintained classical MCM-loader activity but abrogated the array-generation activity of ORC. These mutations impaired replication through chromatin in vitro and were lethal in vivo. Our results establish that ORC, in addition to its canonical role as the MCM loader, has a second crucial function as a master regulator of nucleosome organization at the replication origin, a crucial prerequisite for efficient chromosome replication.
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Affiliation(s)
- Erika Chacin
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Karl-Uwe Reusswig
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jessica Furtmeier
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Priyanka Bansal
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Leonhard A Karl
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
| | - Boris Pfander
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute of Genome Stability in Aging and Disease, CECAD, University of Cologne, Medical Faculty, Cologne, Germany
| | - Tobias Straub
- Core Facility Bioinformatics, BMC, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Philipp Korber
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Christoph F Kurat
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany.
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Nucleosome Remodeling at the Yeast PHO8 and PHO84 Promoters without the Putatively Essential SWI/SNF Remodeler. Int J Mol Sci 2023; 24:ijms24054949. [PMID: 36902382 PMCID: PMC10003099 DOI: 10.3390/ijms24054949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/14/2023] [Accepted: 02/19/2023] [Indexed: 03/08/2023] Open
Abstract
Chromatin remodeling by ATP-dependent remodeling enzymes is crucial for all genomic processes, like transcription or replication. Eukaryotes harbor many remodeler types, and it is unclear why a given chromatin transition requires more or less stringently one or several remodelers. As a classical example, removal of budding yeast PHO8 and PHO84 promoter nucleosomes upon physiological gene induction by phosphate starvation essentially requires the SWI/SNF remodeling complex. This dependency on SWI/SNF may indicate specificity in remodeler recruitment, in recognition of nucleosomes as remodeling substrate or in remodeling outcome. By in vivo chromatin analyses of wild type and mutant yeast under various PHO regulon induction conditions, we found that overexpression of the remodeler-recruiting transactivator Pho4 allowed removal of PHO8 promoter nucleosomes without SWI/SNF. For PHO84 promoter nucleosome removal in the absence of SWI/SNF, an intranucleosomal Pho4 site, which likely altered the remodeling outcome via factor binding competition, was required in addition to such overexpression. Therefore, an essential remodeler requirement under physiological conditions need not reflect substrate specificity, but may reflect specific recruitment and/or remodeling outcomes.
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42
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Neumann H, Jeronimo C, Lucier JF, Pasquier E, Robert F, Wellinger RJ, Gaudreau L. The Histone Variant H2A.Z C-Terminal Domain Has Locus-Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization. Microbiol Spectr 2023; 11:e0255022. [PMID: 36815792 PMCID: PMC10100702 DOI: 10.1128/spectrum.02550-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/05/2023] [Indexed: 02/24/2023] Open
Abstract
The incorporation of histone variant H2A.Z into nucleosomes creates specialized chromatin domains that regulate DNA-templated processes, such as gene transcription. In Saccharomyces cerevisiae, the diverging H2A.Z C terminus is thought to provide the H2A.Z exclusive functions. To elucidate the roles of this H2A.Z C terminus genome-wide, we used derivatives in which the C terminus was replaced with the corresponding region of H2A (ZA protein), or the H2A region plus a transcriptional activating peptide (ZA-rII'), with the intent of regenerating the H2A.Z-dependent regulation globally. The distribution of these H2A.Z derivatives indicates that the H2A.Z C-terminal region is crucial for both maintaining the occupation level of H2A.Z and the proper positioning of targeted nucleosomes. Interestingly, the specific contribution on incorporation efficiency versus nucleosome positioning varies enormously depending on the locus analyzed. Specifically, the role of H2A.Z in global transcription regulation relies on its C-terminal region. Remarkably, however, this mostly involves genes without a H2A.Z nucleosome in the promoter. Lastly, we demonstrate that the main chaperone complex which deposits H2A.Z to gene regulatory region (SWR1-C) is necessary to localize all H2A.Z derivatives at their specific loci, indicating that the differential association of these derivatives is not due to impaired interaction with SWR1-C. IMPORTANCE We provide evidence that the Saccharomyces cerevisiae C-terminal region of histone variant H2A.Z can mediate its special function in performing gene regulation by interacting with effector proteins and chaperones. These functional interactions allow H2A.Z not only to incorporate to very specific gene regulatory regions, but also to facilitate the gene expression process. To achieve this, we used a chimeric protein which lacks the native H2A.Z C-terminal region but contains an acidic activating region, a module that is known to interact with components of chromatin-remodeling entities and/or transcription modulators. We reasoned that because this activating region can fulfill the role of the H2A.Z C-terminal region, at least in part, the role of the latter would be to interact with these activating region targets.
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Affiliation(s)
- Hannah Neumann
- Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Celia Jeronimo
- Montreal Clinical Research Institute, Montréal, Quebec, Canada
| | - Jean-François Lucier
- Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Emeline Pasquier
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - François Robert
- Montreal Clinical Research Institute, Montréal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Luc Gaudreau
- Department of Biology, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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43
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Ciafrè SA, Russo M, Michienzi A, Galardi S. Long Noncoding RNAs and Cancer Stem Cells: Dangerous Liaisons Managing Cancer. Int J Mol Sci 2023; 24:ijms24031828. [PMID: 36768150 PMCID: PMC9915130 DOI: 10.3390/ijms24031828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Decades of research have investigated the mechanisms that lead to the origin of cancer, striving to identify tumor-initiating cells. These cells, also known as cancer stem cells, are characterized by the ability to self-renew, to give rise to differentiated tumor populations, and on a larger scale, are deemed responsible not only for tumor initiation but also for recurrent tumors, often resistant to chemotherapy and radiotherapy. Long noncoding RNAs are RNA molecules longer than 200 nt, lacking the ability to code for proteins, with recognized roles as fine regulators of gene expression. They can exert these functions through a variety of mechanisms, acting at almost all steps of gene expression, from modulation of the epigenetic state of chromatin to modulation of protein stability. In all cases, lncRNAs do not work alone, but they always interact with other RNA molecules, either coding or non-coding, or with protein factors. In this review, we summarize the latest results obtained about the involvement of lncRNAs in the initiating cells of several types of tumors, and highlight the different mechanisms through which they work, while discussing how the modulation of a lncRNA can affect several aspects of tumor onset and progression.
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Affiliation(s)
- Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (S.A.C.); (S.G.)
| | - Monia Russo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Silvia Galardi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (S.A.C.); (S.G.)
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44
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Kunert F, Metzner FJ, Jung J, Höpfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP. Structural mechanism of extranucleosomal DNA readout by the INO80 complex. SCIENCE ADVANCES 2022; 8:eadd3189. [PMID: 36490333 PMCID: PMC9733932 DOI: 10.1126/sciadv.add3189] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.
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Affiliation(s)
- Franziska Kunert
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Felix J. Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - James Jung
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Höpfler
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stephan Woike
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kevin Schall
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Kostrewa
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Manuela Moldt
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Susanne Bantele
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Eustermann
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Corresponding author.
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45
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Basu A, Bobrovnikov DG, Cieza B, Arcon JP, Qureshi Z, Orozco M, Ha T. Deciphering the mechanical code of the genome and epigenome. Nat Struct Mol Biol 2022; 29:1178-1187. [PMID: 36471057 PMCID: PMC10142808 DOI: 10.1038/s41594-022-00877-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications. Deciphering this mechanical code (that is, this dependence) has been challenging due to the lack of high-throughput experimental methods. Here we present a comprehensive characterization of the mechanical code. Utilizing high-throughput measurements of DNA bendability via loop-seq, we quantitatively established how the occurrence and spatial distribution of dinucleotides, tetranucleotides and methylated CpG impact DNA bendability. We used our measurements to develop a physical model for the sequence and methylation dependence of DNA bendability. We validated the model by performing loop-seq on mouse genomic sequences around transcription start sites and CTCF-binding sites. We applied our model to test the predictions of all-atom molecular dynamics simulations and to demonstrate that sequence and epigenetic modifications can mechanically encode regulatory information in diverse contexts.
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Affiliation(s)
- Aakash Basu
- Department of Biosciences, Durham University, Durham, UK. .,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Dmitriy G Bobrovnikov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Basilio Cieza
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Juan Pablo Arcon
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Zan Qureshi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biochemistry and Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 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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46
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
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Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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47
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Hendy O, Serebreni L, Bergauer K, Muerdter F, Huber L, Nemčko F, Stark A. Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers. Mol Cell 2022; 82:3598-3612.e7. [PMID: 36113480 PMCID: PMC7614073 DOI: 10.1016/j.molcel.2022.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/13/2022] [Accepted: 08/17/2022] [Indexed: 01/21/2023]
Abstract
Gene transcription is a highly regulated process in all animals. In Drosophila, two major transcriptional programs, housekeeping and developmental, have promoters with distinct regulatory compatibilities and nucleosome organization. However, it remains unclear how the differences in chromatin structure relate to the distinct regulatory properties and which chromatin remodelers are required for these programs. Using rapid degradation of core remodeler subunits in Drosophila melanogaster S2 cells, we demonstrate that developmental gene transcription requires SWI/SNF-type complexes, primarily to maintain distal enhancer accessibility. In contrast, wild-type-level housekeeping gene transcription requires the Iswi and Ino80 remodelers to maintain nucleosome positioning and phasing at promoters. These differential remodeler dependencies relate to different DNA-sequence-intrinsic nucleosome affinities, which favor a default ON state for housekeeping but a default OFF state for developmental gene transcription. Overall, our results demonstrate how different transcription-regulatory strategies are implemented by DNA sequence, chromatin structure, and remodeler activity.
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Affiliation(s)
- Oliver Hendy
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Leonid Serebreni
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Katharina Bergauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Felix Muerdter
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Lukas Huber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Filip Nemčko
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna, Medical University of Vienna, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Medical University of Vienna, Vienna BioCenter (VBC), Vienna 1030, Austria.
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48
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Diego-Martin B, Pérez-Alemany J, Candela-Ferre J, Corbalán-Acedo A, Pereyra J, Alabadí D, Jami-Alahmadi Y, Wohlschlegel J, Gallego-Bartolomé J. The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis. Nucleic Acids Res 2022; 50:10399-10417. [PMID: 36189880 PMCID: PMC9561266 DOI: 10.1093/nar/gkac826] [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: 06/05/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 11/14/2022] Open
Abstract
Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically incorporates the MINUSCULE (MINU) catalytic subunits and the TRIPLE PHD FINGERS (TPF) signature subunits. Here we report experimental evidence that establishes the functional relevance of TPF proteins for the complex activity. Our results show that depletion of TPF triggers similar pleiotropic phenotypes and molecular defects to those found in minu mutants. Moreover, we report the genomic location of MINU2 and TPF proteins as representative members of this SWI/SNF complex and their impact on nucleosome positioning and transcription. These analyses unravel the binding of the complex to thousands of genes where it modulates the position of the +1 nucleosome. These targets tend to produce 5′-shifted transcripts in the tpf and minu mutants pointing to the participation of the complex in alternative transcription start site usage. Interestingly, there is a remarkable correlation between +1 nucleosome shift and 5′ transcript length change suggesting their functional connection. In summary, this study unravels the function of a plant SWI/SNF complex involved in +1 nucleosome positioning and transcription start site determination.
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Affiliation(s)
- Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Joan Candela-Ferre
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Antonio Corbalán-Acedo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Juan Pereyra
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
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49
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Wu AC, Vivori C, Patel H, Sideri T, Moretto F, van Werven FJ. RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription. Life Sci Alliance 2022; 5:e202201394. [PMID: 36114005 PMCID: PMC9481977 DOI: 10.26508/lsa.202201394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
The directionality of gene promoters-the ratio of protein-coding over divergent noncoding transcription-is highly variable. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription relative to protein-coding transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus to a decrease in promoter directionality. We find that RSC has a modest effect on nucleosome positioning upstream in promoters at the sites of divergent transcription. These promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 DNA-binding protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription relative to coding direction transcription. We propose that any DNA-binding factor, when stably associated with cryptic transcription start sites, forms a barrier which represses divergent transcription, thereby promoting promoter directionality.
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Affiliation(s)
- Andrew Ck Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Vivori
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Theodora Sideri
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
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50
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Mittal C, Lang O, Lai WKM, Pugh BF. An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters. Genes Dev 2022; 36:985-1001. [PMID: 36302553 PMCID: PMC9732905 DOI: 10.1101/gad.350026.122] [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: 09/08/2022] [Accepted: 10/11/2022] [Indexed: 02/05/2023]
Abstract
Genome-wide, little is understood about how proteins organize at inducible promoters before and after induction and to what extent inducible and constitutive architectures depend on cofactors. We report that sequence-specific transcription factors and their tethered cofactors (e.g., SAGA [Spt-Ada-Gcn5-acetyltransferase], Mediator, TUP, NuA4, SWI/SNF, and RPD3-L) are generally bound to promoters prior to induction ("poised"), rather than recruited upon induction, whereas induction recruits the preinitiation complex (PIC) to DNA. Through depletion and/or deletion experiments, we show that SAGA does not function at constitutive promoters, although a SAGA-independent Gcn5 acetylates +1 nucleosomes there. When inducible promoters are poised, SAGA catalyzes +1 nucleosome acetylation but not PIC assembly. When induced, SAGA catalyzes acetylation, deubiquitylation, and PIC assembly. Surprisingly, SAGA mediates induction by creating a PIC that allows TFIID (transcription factor II-D) to stably associate, rather than creating a completely TFIID-independent PIC, as generally thought. These findings suggest that inducible systems, where present, are integrated with constitutive systems.
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Affiliation(s)
- Chitvan Mittal
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Olivia Lang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - William K M Lai
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
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