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Gurgo J, Walter JC, Fiche JB, Houbron C, Schaeffer M, Cavalli G, Bantignies F, Nollmann M. Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes. Cell Rep 2024; 43:114167. [PMID: 38691452 DOI: 10.1016/j.celrep.2024.114167] [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: 04/22/2022] [Revised: 02/15/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024] Open
Abstract
Polycomb (Pc) group proteins are transcriptional regulators with key roles in development, cell identity, and differentiation. Pc-bound chromatin regions form repressive domains that interact in 3D to assemble repressive nuclear compartments. Here, we use multiplexed chromatin imaging to investigate whether Pc compartments involve the clustering of multiple Pc domains during Drosophila development. Notably, 3D proximity between Pc targets is rare and involves predominantly pairwise interactions. These 3D proximities are particularly enhanced in segments where Pc genes are co-repressed. In addition, segment-specific expression of Hox Pc targets leads to their spatial segregation from Pc-repressed genes. Finally, non-Hox Pc targets are more proximal in regions where they are co-expressed. These results indicate that long-range Pc interactions are temporally and spatially regulated during differentiation and development but do not induce frequent clustering of multiple distant Pc genes.
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Affiliation(s)
- Julian Gurgo
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Université de Montpellier, CNRS, Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Christophe Houbron
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Marie Schaeffer
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France
| | - Giacomo Cavalli
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Frédéric Bantignies
- Institut de Génétique Humaine, CNRS UMR 9002, Université de Montpellier, 141 rue de la Cardonille, 34396 Montpellier, France.
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellier, 60 rue de Navacelles, 34090 Montpellier, France.
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2
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Vorobyeva NE, Krasnov AN, Erokhin M, Chetverina D, Mazina M. Su(Hw) interacts with Combgap to establish long-range chromatin contacts. Epigenetics Chromatin 2024; 17:17. [PMID: 38773468 PMCID: PMC11106861 DOI: 10.1186/s13072-024-00541-x] [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: 01/29/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) insulator-binding protein to genome topology remains unclear. RESULTS In this study, we provide evidence for the existence of long-range interactions between chromatin bound Su(Hw) and Combgap, which was first characterised as Polycomb response elements binding protein. Loss of Su(Hw) binding to chromatin results in the disappearance of Su(Hw)-Combgap long-range interactions and in a decrease in spatial self-interactions among a subset of Su(Hw)-bound genome sites. Our findings suggest that Su(Hw)-Combgap long-range interactions are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators' binding. CONCLUSIONS This study demonstrates that Su(Hw) insulator binding protein can form long-range interactions with Combgap, Polycomb response elements binding protein, and that these interactions are associated with active chromatin factors rather than with Polycomb dependent repression.
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Affiliation(s)
- Nadezhda E Vorobyeva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alexey N Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Marina Mazina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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3
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Kahn TG, Savitsky M, Kuong C, Jacquier C, Cavalli G, Chang JM, Schwartz YB. Topological screen identifies hundreds of Cp190- and CTCF-dependent Drosophila chromatin insulator elements. SCIENCE ADVANCES 2023; 9:eade0090. [PMID: 36735780 PMCID: PMC9897668 DOI: 10.1126/sciadv.ade0090] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Drosophila insulators were the first DNA elements found to regulate gene expression by delimiting chromatin contacts. We still do not know how many of them exist and what impact they have on the Drosophila genome folding. Contrary to vertebrates, there is no evidence that fly insulators block cohesin-mediated chromatin loop extrusion. Therefore, their mechanism of action remains uncertain. To bridge these gaps, we mapped chromatin contacts in Drosophila cells lacking the key insulator proteins CTCF and Cp190. With this approach, we found hundreds of insulator elements. Their study indicates that Drosophila insulators play a minor role in the overall genome folding but affect chromatin contacts locally at many loci. Our observations argue that Cp190 promotes cobinding of other insulator proteins and that the model, where Drosophila insulators block chromatin contacts by forming loops, needs revision. Our insulator catalog provides an important resource to study mechanisms of genome folding.
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Affiliation(s)
- Tatyana G. Kahn
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | | | - Chikuan Kuong
- Department of Computer Science, National Chengchi University, Taipei City, Taiwan
| | | | - Giacomo Cavalli
- Institute of Human Genetics, UMR9002 CNRS, Montpellier, France
| | - Jia-Ming Chang
- Department of Computer Science, National Chengchi University, Taipei City, Taiwan
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4
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Mora A, Huang X, Jauhari S, Jiang Q, Li X. Chromatin Hubs: A biological and computational outlook. Comput Struct Biotechnol J 2022; 20:3796-3813. [PMID: 35891791 PMCID: PMC9304431 DOI: 10.1016/j.csbj.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/02/2022] [Accepted: 07/02/2022] [Indexed: 11/20/2022] Open
Abstract
This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease.
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Affiliation(s)
- Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
- Corresponding authors.
| | - Xiaowei Huang
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Shaurya Jauhari
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Qin Jiang
- Affiliated Eye Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, and Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China
- Corresponding authors.
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5
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Ilyin AA, Kononkova AD, Golova AV, Shloma VV, Olenkina O, Nenasheva V, Abramov Y, Kotov AA, Maksimov D, Laktionov P, Pindyurin A, Galitsyna A, Ulianov S, Khrameeva E, Gelfand M, Belyakin S, Razin S, Shevelyov Y. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3203-3225. [PMID: 35166842 PMCID: PMC8989536 DOI: 10.1093/nar/gkac109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis – in bamΔ86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters’ detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.
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Affiliation(s)
| | | | | | | | | | - Valentina V Nenasheva
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Yuri A Abramov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Alexei A Kotov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Daniil A Maksimov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Petr P Laktionov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ekaterina E Khrameeva
- Correspondence may also be addressed to Ekaterina Khrameeva. Tel: +7 495 2801481; Fax: +7 495 2801481;
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Stepan N Belyakin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Yuri Y Shevelyov
- To whom correspondence should be addressed. Tel: +7 499 1960809; Fax: +7 499 1960221;
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6
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Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes. Epigenetics Chromatin 2020; 13:41. [PMID: 33028366 PMCID: PMC7541242 DOI: 10.1186/s13072-020-00358-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 09/15/2020] [Indexed: 01/04/2023] Open
Abstract
Background Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. The regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. Emerging evidence suggests that genome organization and transcriptional regulation are inter-linked. However, the pericentromeric genome organization is relatively less studied. Therefore, we sought to characterize the pericentromeric genome organization and understand how this organization along with the pericentromeric factors influences heterochromatic gene expression. Results Here, we characterized the pericentromeric genome organization in Drosophila melanogaster using 5C sequencing. Heterochromatic topologically associating domains (Het TADs) correlate with distinct epigenomic domains of active and repressed heterochromatic genes at the pericentromeres. These genes are known to depend on the heterochromatic landscape for their expression. However, HP1a or Su(var)3-9 RNAi has minimal effects on heterochromatic gene expression, despite causing significant changes in the global Het TAD organization. Probing further into this observation, we report the role of two other chromatin proteins enriched at the pericentromeres-dMES-4 and dADD1 in regulating the expression of a subset of heterochromatic genes. Conclusions Distinct pericentromeric genome organization and chromatin landscapes maintained by the interplay of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) are sufficient to support heterochromatic gene expression despite the loss of global Het TAD structure. These findings open new avenues for future investigations into the mechanisms of heterochromatic gene expression.
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7
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Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Tidying-up the plant nuclear space: domains, functions, and dynamics. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5160-5178. [PMID: 32556244 PMCID: PMC8604271 DOI: 10.1093/jxb/eraa282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova
de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České
Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České
Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de
Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir
University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of
Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart,
Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The
Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway,
Galway, Ireland
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8
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Viets K, Sauria MEG, Chernoff C, Rodriguez Viales R, Echterling M, Anderson C, Tran S, Dove A, Goyal R, Voortman L, Gordus A, Furlong EEM, Taylor J, Johnston RJ. Characterization of Button Loci that Promote Homologous Chromosome Pairing and Cell-Type-Specific Interchromosomal Gene Regulation. Dev Cell 2019; 51:341-356.e7. [PMID: 31607649 DOI: 10.1016/j.devcel.2019.09.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 06/07/2019] [Accepted: 09/09/2019] [Indexed: 01/05/2023]
Abstract
Homologous chromosomes colocalize to regulate gene expression in processes including genomic imprinting, X-inactivation, and transvection. In Drosophila, homologous chromosomes pair throughout development, promoting transvection. The "button" model of pairing proposes that specific regions along chromosomes pair with high affinity. Here, we identify buttons interspersed across the fly genome that pair with their homologous sequences, even when relocated to multiple positions in the genome. A majority of transgenes that span a full topologically associating domain (TAD) function as buttons, but not all buttons contain TADs. Additionally, buttons are enriched for insulator protein clusters. Fragments of buttons do not pair, suggesting that combinations of elements within a button are required for pairing. Pairing is necessary but not sufficient for transvection. Additionally, pairing and transvection are stronger in some cell types than in others, suggesting that pairing strength regulates transvection efficiency between cell types. Thus, buttons pair homologous chromosomes to facilitate cell-type-specific interchromosomal gene regulation.
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Affiliation(s)
- Kayla Viets
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael E G Sauria
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chaim Chernoff
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Max Echterling
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Caitlin Anderson
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sang Tran
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Abigail Dove
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Raghav Goyal
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lukas Voortman
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew Gordus
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Eileen E M Furlong
- European Molecular Biology Laboratory, Department of Genome Biology, Heidelberg 69117, Germany
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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9
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Voigt S, Erpf AC, Stephan W. Decreased Temperature Sensitivity of Vestigial Gene Expression in Temperate Populations of Drosophila melanogaster. Genes (Basel) 2019; 10:genes10070498. [PMID: 31261809 PMCID: PMC6679080 DOI: 10.3390/genes10070498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Accepted: 06/21/2019] [Indexed: 11/24/2022] Open
Abstract
Drosophila melanogaster recently spread from its tropical origin in Africa and became a cosmopolitan species that has adapted to a wide range of different thermal environments, including temperate climates. An important limiting factor of temperate climates has probably been their low and varying temperatures. The transcriptional output of genes can vary across temperatures, which might have been detrimental while settling in temperate environments. The reduction of temperature-sensitive expression of functionally important genes to ensure consistent levels of gene expression might have been relevant while adapting to such environments. In this study, we focus on the gene vestigial (vg) whose product is a key factor in wing development. We provide evidence that temperature-sensitivity of vg has been buffered in populations from temperate climates. We investigated temperature-sensitivity of vg gene expression in six natural populations, including four temperate populations (three from Europe and one from high-altitude Africa), and two tropical populations from the ancestral species range. All temperate populations exhibited a lower degree of temperature-induced expression plasticity than the tropical populations.
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Affiliation(s)
- Susanne Voigt
- Section of Evolutionary Biology, Department of Biology II, University of Munich, 82152 Planegg-Martinsried, Germany.
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, 01217 Dresden, Germany.
| | - Anna Christina Erpf
- Section of Evolutionary Biology, Department of Biology II, University of Munich, 82152 Planegg-Martinsried, Germany.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada.
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, University of Munich, 82152 Planegg-Martinsried, Germany.
- Leibniz Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany.
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10
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Vorobyeva NE, Mazina MY. Functions of Insulators in the Context of Modern Whole-Genome Investigations. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419020170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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11
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Chathoth KT, Zabet NR. Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome. Genome Res 2019; 29:613-625. [PMID: 30709849 PMCID: PMC6442379 DOI: 10.1101/gr.246710.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/23/2019] [Indexed: 12/14/2022]
Abstract
The organization of the genome into topologically associating domains (TADs) was shown to have a regulatory role in development and cellular function, but the mechanism involved in TAD establishment is still unclear. Here, we present the first high-resolution contact map of Drosophila neuronal cells (BG3) and identify different classes of TADs by comparing this to genome organization in embryonic cells (Kc167). We find that only some TADs are conserved in both cell lines, whereas the rest are cell-type–specific. This is supported by a change in the enrichment of architectural proteins at TAD borders, with BEAF-32 present in embryonic cells and CTCF in neuronal cells. Furthermore, we observe strong divergent transcription, together with RNA Polymerase II occupancy and an increase in DNA accessibility at the TAD borders. TAD borders that are specific to neuronal cells are enriched in enhancers controlled by neuronal-specific transcription factors. Our results suggest that TADs are dynamic across developmental stages and reflect the interplay between insulators, transcriptional states, and enhancer activities.
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Affiliation(s)
- Keerthi T Chathoth
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Nicolae Radu Zabet
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
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12
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Vermunt MW, Zhang D, Blobel GA. The interdependence of gene-regulatory elements and the 3D genome. J Cell Biol 2019; 218:12-26. [PMID: 30442643 PMCID: PMC6314554 DOI: 10.1083/jcb.201809040] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 01/12/2023] Open
Abstract
Imaging studies, high-resolution chromatin conformation maps, and genome-wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene expression. Cross-talk between gene-regulatory elements is often organized within insulated neighborhoods, and regulatory cues that induce transcriptional changes can reshape chromatin folding patterns and gene positioning within the nucleus. The cause-consequence relationship of genome architecture and gene expression is intricate, and its molecular mechanisms are under intense investigation. Here, we review the interdependency of transcription and genome organization with emphasis on enhancer-promoter contacts in gene regulation.
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Affiliation(s)
- Marit W Vermunt
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Di Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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13
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Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster. Sci Rep 2018; 8:15685. [PMID: 30356106 PMCID: PMC6200757 DOI: 10.1038/s41598-018-34115-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/08/2018] [Indexed: 12/21/2022] Open
Abstract
Increasing lines of evidence support that Argonaute2 (AGO2) harbors several nuclear functions in metazoa. In particular, Drosophila AGO2 modulates transcription of developmentally regulated genes; however, the molecular mechanisms behind AGO2 recruitment into chromatin and its function in transcription have not been deeply explored. In this study, we show that Drosophila AGO2 chromatin association depends on active transcription. In order to gain insight into how AGO2 controls transcription, we performed differential ChIP-seq analysis for RNA Polymerase II (Pol II) upon depletion of AGO2. Remarkably, we find specific accumulation of the elongating but not initiating form of Pol II after AGO2 knockdown, suggesting that AGO2 impairs transcription elongation. Finally, AGO2 also affects Negative Elongation Factor (NELF) chromatin association but not the Cyclin Dependent Kinase 9 (CDK9). Altogether, these results provide key insights into the molecular role of AGO2 in attenuating elongation of certain actively transcribed genes.
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14
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La Fortezza M, Grigolon G, Cosolo A, Pindyurin A, Breimann L, Blum H, van Steensel B, Classen AK. DamID profiling of dynamic Polycomb-binding sites in Drosophila imaginal disc development and tumorigenesis. Epigenetics Chromatin 2018; 11:27. [PMID: 29871666 PMCID: PMC5987561 DOI: 10.1186/s13072-018-0196-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/21/2018] [Indexed: 02/06/2023] Open
Abstract
Background Tracking dynamic protein–chromatin interactions in vivo is key to unravel transcriptional and epigenetic transitions in development and disease. However, limited availability and heterogeneous tissue composition of in vivo source material impose challenges on many experimental approaches. Results Here we adapt cell-type-specific DamID-seq profiling for use in Drosophila imaginal discs and make FLP/FRT-based induction accessible to GAL driver-mediated targeting of specific cell lineages. In a proof-of-principle approach, we utilize ubiquitous DamID expression to describe dynamic transitions of Polycomb-binding sites during wing imaginal disc development and in a scrib tumorigenesis model. We identify Atf3 and Ets21C as novel Polycomb target genes involved in scrib tumorigenesis and suggest that target gene regulation by Atf3 and AP-1 transcription factors, as well as modulation of insulator function, plays crucial roles in dynamic Polycomb-binding at target sites. We establish these findings by DamID-seq analysis of wing imaginal disc samples derived from 10 larvae. Conclusions Our study opens avenues for robust profiling of small cell population in imaginal discs in vivo and provides insights into epigenetic changes underlying transcriptional responses to tumorigenic transformation. Electronic supplementary material The online version of this article (10.1186/s13072-018-0196-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco La Fortezza
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Department of Environmental Systems Science, ETH Zurich, Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Giovanna Grigolon
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Department of Health Sciences and Technology, ETH Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
| | - Andrea Cosolo
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Alexey Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Laura Breimann
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center Munich, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377, Munich, Germany
| | - Bas van Steensel
- Division Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Anne-Kathrin Classen
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Planegg, Martinsried, Germany. .,Center for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.
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15
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Sharakhov IV, Bondarenko SM, Artemov GN, Onufriev AV. The Role of Chromosome–Nuclear Envelope Attachments in 3D Genome Organization. BIOCHEMISTRY (MOSCOW) 2018; 83:350-358. [DOI: 10.1134/s0006297918040065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Nazer E, Dale RK, Chinen M, Radmanesh B, Lei EP. Argonaute2 and LaminB modulate gene expression by controlling chromatin topology. PLoS Genet 2018. [PMID: 29529026 PMCID: PMC5864089 DOI: 10.1371/journal.pgen.1007276] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Drosophila Argonaute2 (AGO2) has been shown to regulate expression of certain loci in an RNA interference (RNAi)-independent manner, but its genome-wide function on chromatin remains unknown. Here, we identified the nuclear scaffolding protein LaminB as a novel interactor of AGO2. When either AGO2 or LaminB are depleted in Kc cells, similar transcription changes are observed genome-wide. In particular, changes in expression occur mainly in active or potentially active chromatin, both inside and outside LaminB-associated domains (LADs). Furthermore, we identified a somatic target of AGO2 transcriptional repression, no hitter (nht), which is immersed in a LAD located within a repressive topologically-associated domain (TAD). Null mutation but not catalytic inactivation of AGO2 leads to ectopic expression of nht and downstream spermatogenesis genes. Depletion of either AGO2 or LaminB results in reduced looping interactions within the nht TAD as well as ectopic inter-TAD interactions, as detected by 4C-seq analysis. Overall, our findings reveal coordination of AGO2 and LaminB function to dictate genome architecture and thereby regulate gene expression. Argonaute proteins are an evolutionarily conserved protein family engaged in gene silencing. The key RNA interference (RNAi) pathway protein AGO2 interacts with small RNAs to regulate gene silencing in the cytoplasm. In addition, AGO2 has been shown to regulate gene expression by functioning in the nucleus. In this study, we determined that AGO2 forms a nuclear complex with LaminB, a nuclear scaffolding protein, as well as the transcription machinery. Together, AGO2 and LaminB limit transcription in active or potentially active regions that either do or do not interact directly with the nuclear lamina. We focused on nht, a master control gene of the sperm developmental program, which is up-regulated in the absence of AGO2 or LaminB. The nht gene interacts with the nuclear lamina in somatic cells, and we determined that AGO2 and LaminB control the three-dimensional configuration of the chromatin region in which nht is located. We conclude that AGO2 and LaminB work in concert to regulate how genes are turned on or off by controlling how the genome is folded within the nucleus, and therefore can affect key developmental processes such as the production of sperm.
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Affiliation(s)
- Ezequiel Nazer
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rockville Pike, Bethesda, MD, United States of America
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rockville Pike, Bethesda, MD, United States of America
| | - Ryan K. Dale
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rockville Pike, Bethesda, MD, United States of America
| | - Madoka Chinen
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rockville Pike, Bethesda, MD, United States of America
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rockville Pike, Bethesda, MD, United States of America
| | - Behram Radmanesh
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rockville Pike, Bethesda, MD, United States of America
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rockville Pike, Bethesda, MD, United States of America
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Rockville Pike, Bethesda, MD, United States of America
- * E-mail:
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17
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Misale MS, Witek Janusek L, Tell D, Mathews HL. Chromatin organization as an indicator of glucocorticoid induced natural killer cell dysfunction. Brain Behav Immun 2018; 67:279-289. [PMID: 28911980 PMCID: PMC5696065 DOI: 10.1016/j.bbi.2017.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/01/2017] [Accepted: 09/08/2017] [Indexed: 11/19/2022] Open
Abstract
It is well-established that psychological distress reduces natural killer cell immune function and that this reduction can be due to the stress-induced release of glucocorticoids. Glucocorticoids are known to alter epigenetic marks associated with immune effector loci, and are also known to influence chromatin organization. The purpose of this investigation was to assess the effect of glucocorticoids on natural killer cell chromatin organization and to determine the relationship of chromatin organization to natural killer cell effector function, e.g. interferon gamma production. Interferon gamma production is the prototypic cytokine produced by natural killer cells and is known to modulate both innate and adaptive immunity. Glucocorticoid treatment of human peripheral blood mononuclear cells resulted in a significant reduction in interferon gamma production. Glucocorticoid treatment also resulted in a demonstrable natural killer cell nuclear phenotype. This phenotype was localization of the histone, post-translational epigenetic mark, H3K27me3, to the nuclear periphery. Peripheral nuclear localization of H3K27me3 was directly related to cellular levels of interferon gamma. This nuclear phenotype was determined by direct visual inspection and by use of an automated, high through-put technology, the Amnis ImageStream. This technology combines the per-cell information content provided by standard microscopy with the statistical significance afforded by large sample sizes common to standard flow cytometry. Most importantly, this technology provides for a direct assessment of the localization of signal intensity within individual cells. The results demonstrate glucocorticoids to dysregulate natural killer cell function at least in part through altered H3K27me3 nuclear organization and demonstrate H3K27me3 chromatin organization to be a predictive indicator of glucocorticoid induced immune dysregulation of natural killer cells.
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Affiliation(s)
- Michael S Misale
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States
| | - Linda Witek Janusek
- Marcella Niehoff School of Nursing, Department of Health Promotion, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States
| | - Dina Tell
- Marcella Niehoff School of Nursing, Department of Health Promotion, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States
| | - Herbert L Mathews
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States.
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18
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An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx/MLL/COMPASS. Mol Cell 2017; 63:318-328. [PMID: 27447986 DOI: 10.1016/j.molcel.2016.06.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 04/07/2016] [Accepted: 06/10/2016] [Indexed: 12/20/2022]
Abstract
Polycomb response elements (PREs) are specific DNA sequences that stably maintain the developmental pattern of gene expression. Drosophila PREs are well characterized, whereas the existence of PREs in mammals remains debated. Accumulating evidence supports a model in which CpG islands recruit Polycomb group (PcG) complexes; however, which subset of CGIs is selected to serve as PREs is unclear. Trithorax (Trx) positively regulates gene expression in Drosophila and co-occupies PREs to antagonize Polycomb-dependent silencing. Here we demonstrate that Trx-dependent H3K4 dimethylation (H3K4me2) marks Drosophila PREs and maintains the developmental expression pattern of nearby genes. Similarly, the mammalian Trx homolog, MLL1, deposits H3K4me2 at CpG-dense regions that could serve as PREs. In the absence of MLL1 and H3K4me2, H3K27me3 levels, a mark of Polycomb repressive complex 2 (PRC2), increase at these loci. By inhibiting PRC2-dependent H3K27me3 in the absence of MLL1, we can rescue expression of these loci, demonstrating a functional balance between MLL1 and PRC2 activities at these sites. Thus, our study provides rules for identifying cell-type-specific functional mammalian PREs within the human genome.
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19
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Sex combs reduced (Scr) regulatory region of Drosophila revisited. Mol Genet Genomics 2017; 292:773-787. [DOI: 10.1007/s00438-017-1309-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/08/2017] [Indexed: 10/19/2022]
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20
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Haithem H, Ons A, Salma N, Jihène R, Mariam A, Mariem M, Mariem N, Nabila BR, Asma O, Sana BA, Sofien B, Ali B. Association between dementia and vascular disease-associated polymorphisms in a Tunisian population. Int J Neurosci 2017; 128:32-41. [PMID: 28657841 DOI: 10.1080/00207454.2017.1348353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE Dementia is a multifactorial idiopathic pathology caused by clinical, eDementia is a multifactorial idiopathic pathology caused by clinical, environmental and genetic factors. Hence, its etiology is still unknown. We aimed to evaluate the association between five genetic risk factors for vascular diseases and dementia individually and when gathered in haplotypes. MATERIALS AND METHOD We enrolled 200 dementia patients and 300 controls. All subjects were genotyped for vascular diseaseassociated polymorphisms in the genes coding for Apolipoprotein-E (ApoE), angiotensin converting enzyme (ACE) and Paraoxonase-1 (PON1). RESULTS The association between dementia risk and all the studied polymorphisms except of PON1-Q192R was found to be significant. Carrying the ApoE e4 allele seems to increase dementia risk by 4.32 fold (p = 0.001). The risk associated with ACE I and PON1-L55M T alleles were lower (2.58 and 2.11 fold, p < 0.001 and p = 0.015, respectively). When combined in haplotypes, these polymorphisms showed a cumulative and synergetic effect. GTICC haplotype appears to be associated with 9-fold dementia risk (p < 0.001), whereas AADTT seems to reduce dementia risk by 80% (p = 0.003). CONCLUSION Our results suggest that, ApoE ε4, ACE I and PON1-L55M T alleles are associated with dementia risk whether these polymorphisms were studied separately or gathered in haplotypes. Still, the contribution of each gene to the pathophysiological development of dementia must be more investigated.
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Affiliation(s)
- Hamdouni Haithem
- a Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia.,d Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
| | - Achour Ons
- a Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia.,d Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
| | - Naija Salma
- b Neurology Department , Sahloul University Hospital , Sousse , Tunisia
| | - Rejeb Jihène
- a Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia
| | - Aounallah Mariam
- a Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia
| | - Mhiri Mariem
- b Neurology Department , Sahloul University Hospital , Sousse , Tunisia
| | - Noureddine Mariem
- a Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia.,d Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
| | - Ben Rejeb Nabila
- a Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia.,c Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia.,d Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
| | - Omezzine Asma
- a Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia.,c Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia.,d Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
| | - Ben Amor Sana
- b Neurology Department , Sahloul University Hospital , Sousse , Tunisia
| | - Benammou Sofien
- b Neurology Department , Sahloul University Hospital , Sousse , Tunisia
| | - Bouslama Ali
- a Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia.,c Biochemistry Department , Sahloul University Hospital , Sousse , Tunisia.,d Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
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21
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Three-Dimensional Genome Organization and Function in Drosophila. Genetics 2017; 205:5-24. [PMID: 28049701 PMCID: PMC5223523 DOI: 10.1534/genetics.115.185132] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/15/2016] [Indexed: 12/18/2022] Open
Abstract
Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques.
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22
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Ciabrelli F, Comoglio F, Fellous S, Bonev B, Ninova M, Szabo Q, Xuéreb A, Klopp C, Aravin A, Paro R, Bantignies F, Cavalli G. Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nat Genet 2017; 49:876-886. [PMID: 28436983 PMCID: PMC5484582 DOI: 10.1038/ng.3848] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/27/2017] [Indexed: 12/15/2022]
Abstract
Transgenerational Epigenetic Inheritance (TEI) studies the transmission of alternative functional states through multiple generations in the presence of the same genomic DNA sequence. Very little is known on the principles and the molecular mechanisms governing this type of inheritance. Here, by transiently enhancing 3D chromatin interactions, we established stable and isogenic Drosophila epilines that carry alternative epialleles, defined by differential levels of the Polycomb-dependent H3K27me3 mark. Once established, epialleles can be dominantly transmitted to naïve flies and induce paramutation. Importantly, epilines can be reset to a naïve state by disrupting chromatin interactions. Finally, we show that environmental changes can modulate the expressivity of the epialleles and we extend our paradigm to naturally occurring phenotypes. Our work sheds light on how nuclear organization and Polycomb group proteins contribute to epigenetically inheritable phenotypic variability.
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Affiliation(s)
- Filippo Ciabrelli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Boyan Bonev
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Maria Ninova
- Division of Biology, California Institute of Technology, Pasadena, California, USA
| | - Quentin Szabo
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | | | - Christophe Klopp
- Unité de Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet Tolosan, France
| | - Alexei Aravin
- Division of Biology, California Institute of Technology, Pasadena, California, USA
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
| | - Frédéric Bantignies
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
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23
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Grob S, Grossniklaus U. Chromosome conformation capture-based studies reveal novel features of plant nuclear architecture. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:149-157. [PMID: 28411415 DOI: 10.1016/j.pbi.2017.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
Nuclear genome organization has recently received increasing attention due to its manifold functions in basic nuclear processes, such as replication, transcription, and the maintenance of genome integrity. Using technologies based on chromosome conformation capture, such as Hi-C, we now have the possibility to study the three-dimensional organization of the genome at unprecedented resolution, shedding light onto a previously unexplored level of nuclear architecture. In plants, research in this field is still in its infancy but a number of publications provided first insights into basic principles of nuclear genome organization and the factors that influence it. Apart from general aspects, newly discovered three-dimensional conformations, such as the KNOT, raise special interest on how nuclear organization may influence the function of the genome in previously unexpected ways.
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Affiliation(s)
- Stefan Grob
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland.
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
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24
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Chromatin proteins and RNA are associated with DNA during all phases of mitosis. Cell Discov 2016; 2:16038. [PMID: 27807477 PMCID: PMC5078801 DOI: 10.1038/celldisc.2016.38] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/07/2016] [Indexed: 12/11/2022] Open
Abstract
Mitosis brings about major changes to chromosome and nuclear structure. We used recently developed proximity ligation assay-based techniques to investigate the association with DNA of chromatin-associated proteins and RNAs in Drosophila embryos during mitosis. All groups of tested proteins, histone-modifying and chromatin-remodeling proteins and methylated histones remained in close proximity to DNA during all phases of mitosis. We also found that RNA transcripts are associated with DNA during all stages of mitosis. Reduction of H3K27me3 levels or elimination of RNAs had no effect on the association of the components of PcG and TrxG complexes to DNA. Using a combination of proximity ligation assay-based techniques and super-resolution microscopy, we found that the number of protein-DNA and RNA-DNA foci undergoes significant reduction during mitosis, suggesting that mitosis may be accompanied by structural re-arrangement or compaction of specific chromatin domains.
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25
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Buxa MK, Slotman JA, van Royen ME, Paul MW, Houtsmuller AB, Renkawitz R. Insulator speckles associated with long-distance chromatin contacts. Biol Open 2016; 5:1266-74. [PMID: 27464669 PMCID: PMC5051650 DOI: 10.1242/bio.019455] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nuclear foci of chromatin binding factors are, in many cases, discussed as sites of long-range chromatin interaction in the three-dimensional nuclear space. Insulator binding proteins have been shown to aggregate into insulator bodies, which are large structures not involved in insulation; however, the more diffusely distributed insulator speckles have not been analysed in this respect. Furthermore, insulator binding proteins have been shown to drive binding sites for Polycomb group proteins into Polycomb bodies. Here we find that insulator speckles, marked by the insulator binding protein dCTCF, and Polycomb bodies show differential association with the insulator protein CP190. They differ in number and three-dimensional location with only 26% of the Polycomb bodies overlapping with CP190. By using fluorescence in situ hybridization (FISH) probes to identify long-range interaction (kissing) of the Hox gene clusters Antennapedia complex (ANT-C) and Bithorax complex (BX-C), we found the frequency of interaction to be very low. However, these rare kissing events were associated with insulator speckles at a significantly shorter distance and an increased speckle number. This suggests that insulator speckles are associated with long-distance interaction.
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Affiliation(s)
- Melanie K Buxa
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, Giessen D35392, Germany
| | - Johan A Slotman
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Maarten W Paul
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, Giessen D35392, Germany
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26
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Entrevan M, Schuettengruber B, Cavalli G. Regulation of Genome Architecture and Function by Polycomb Proteins. Trends Cell Biol 2016; 26:511-525. [PMID: 27198635 DOI: 10.1016/j.tcb.2016.04.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/13/2022]
Abstract
Polycomb group (PcG) proteins dynamically define cellular identities through the epigenetic repression of key developmental regulatory genes. PcG proteins are recruited to specific regulatory elements to modify the chromatin surrounding them. In addition, they regulate the organization of their target genes in the 3D space of the nucleus, and this regulatory function of the 3D genome architecture is involved in cell differentiation and the maintenance of cellular memory. In this review we discuss recent advances in our understanding of how PcG proteins are recruited to chromatin to induce local and global changes in chromosome conformation and regulate their target genes.
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Affiliation(s)
- Marianne Entrevan
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Bernd Schuettengruber
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
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27
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Abstract
Gene expression control is a fundamental determinant of cellular life with transcription being the most important step. The spatial nuclear arrangement of the transcription process driven by RNA polymerases II and III is nonrandomly organized in foci, which is believed to add another regulatory layer on gene expression control. RNA polymerase I transcription takes place within a specialized organelle, the nucleolus. Transcription of ribosomal RNA directly responds to metabolic requirements, which in turn is reflected in the architecture of nucleoli. It differs from that of the other polymerases with respect to the gene template organization, transcription rate, and epigenetic expression control, whereas other features are shared like the formation of DNA loops bringing genes and components of the transcription machinery in close proximity. In recent years, significant advances have been made in the understanding of the structural prerequisites of nuclear transcription, of the arrangement in the nuclear volume, and of the dynamics of these entities. Here, we compare ribosomal RNA and mRNA transcription side by side and review the current understanding focusing on structural aspects of transcription foci, of their constituents, and of the dynamical behavior of these components with respect to foci formation, disassembly, and cell cycle.
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Affiliation(s)
- Klara Weipoltshammer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
| | - Christian Schöfer
- Department for Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
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Wani AH, Boettiger AN, Schorderet P, Ergun A, Münger C, Sadreyev RI, Zhuang X, Kingston RE, Francis NJ. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat Commun 2016; 7:10291. [PMID: 26759081 PMCID: PMC4735512 DOI: 10.1038/ncomms10291] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/26/2015] [Indexed: 12/21/2022] Open
Abstract
The genomes of metazoa are organized at multiple scales. Many proteins that regulate genome architecture, including Polycomb group (PcG) proteins, form subnuclear structures. Deciphering mechanistic links between protein organization and chromatin architecture requires precise description and mechanistic perturbations of both. Using super-resolution microscopy, here we show that PcG proteins are organized into hundreds of nanoscale protein clusters. We manipulated PcG clusters by disrupting the polymerization activity of the sterile alpha motif (SAM) of the PcG protein Polyhomeotic (Ph) or by increasing Ph levels. Ph with mutant SAM disrupts clustering of endogenous PcG complexes and chromatin interactions while elevating Ph level increases cluster number and chromatin interactions. These effects can be captured by molecular simulations based on a previously described chromatin polymer model. Both perturbations also alter gene expression. Organization of PcG proteins into small, abundant clusters on chromatin through Ph SAM polymerization activity may shape genome architecture through chromatin interactions.
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Affiliation(s)
- Ajazul H. Wani
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Alistair N. Boettiger
- Howard Hughes Medical Institute, Harvard University Cambridge, Cambridge, Massachusetts 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Patrick Schorderet
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ayla Ergun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Christine Münger
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - Ruslan I. Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University Cambridge, Cambridge, Massachusetts 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Robert E. Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicole J. Francis
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
- Département de biochimie et medécine moléculaire, Université de Montréal, Montréal, Québec, Canada
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Abstract
Linear chromatin fiber is packed inside the nuclei as a complex three-dimensional structure, and the organization of the chromatin has important roles in the appropriate spatial and temporal regulation of gene expression. To understand how chromatin organizes inside nuclei, and how regulatory proteins physically interact with genes, chromosome conformation capture (3C) technique provides a powerful and sensitive tool to detect both short- and long-range DNA-DNA interaction. Here I describe the 3C technique to detect the DNA-DNA interactions mediated by insulator proteins that are closely related to PcG in Drosophila, which is also broadly applicable to other systems.
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Affiliation(s)
- Hua-Bing Li
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA.
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One, Two, Three: Polycomb Proteins Hit All Dimensions of Gene Regulation. Genes (Basel) 2015; 6:520-42. [PMID: 26184319 PMCID: PMC4584315 DOI: 10.3390/genes6030520] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/30/2015] [Indexed: 12/16/2022] Open
Abstract
Polycomb group (PcG) proteins contribute to the formation and maintenance of a specific repressive chromatin state that prevents the expression of genes in a particular space and time. Polycomb repressive complexes (PRCs) consist of several PcG proteins with specific regulatory or catalytic properties. PRCs are recruited to thousands of target genes, and various recruitment factors, including DNA-binding proteins and non-coding RNAs, are involved in the targeting. PcG proteins contribute to a multitude of biological processes by altering chromatin features at different scales. PcG proteins mediate both biochemical modifications of histone tails and biophysical modifications (e.g., chromatin fiber compaction and three-dimensional (3D) chromatin conformation). Here, we review the role of PcG proteins in nuclear architecture, describing their impact on the structure of the chromatin fiber, on chromatin interactions, and on the spatial organization of the genome in nuclei. Although little is known about the role of plant PcG proteins in nuclear organization, much is known in the animal field, and we highlight similarities and differences in the roles of PcG proteins in 3D gene regulation in plants and animals.
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Hecker A, Brand LH, Peter S, Simoncello N, Kilian J, Harter K, Gaudin V, Wanke D. The Arabidopsis GAGA-Binding Factor BASIC PENTACYSTEINE6 Recruits the POLYCOMB-REPRESSIVE COMPLEX1 Component LIKE HETEROCHROMATIN PROTEIN1 to GAGA DNA Motifs. PLANT PHYSIOLOGY 2015; 168:1013-24. [PMID: 26025051 PMCID: PMC4741334 DOI: 10.1104/pp.15.00409] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/26/2015] [Indexed: 05/19/2023]
Abstract
Polycomb-repressive complexes (PRCs) play key roles in development by repressing a large number of genes involved in various functions. Much, however, remains to be discovered about PRC-silencing mechanisms as well as their targeting to specific genomic regions. Besides other mechanisms, GAGA-binding factors in animals can guide PRC members in a sequence-specific manner to Polycomb-responsive DNA elements. Here, we show that the Arabidopsis (Arabidopsis thaliana) GAGA-motif binding factor protein basic pentacysteine6 (BPC6) interacts with like heterochromatin protein1 (LHP1), a PRC1 component, and associates with vernalization2 (VRN2), a PRC2 component, in vivo. By using a modified DNA-protein interaction enzyme-linked immunosorbant assay, we could show that BPC6 was required and sufficient to recruit LHP1 to GAGA motif-containing DNA probes in vitro. We also found that LHP1 interacts with VRN2 and, therefore, can function as a possible scaffold between BPC6 and VRN2. The lhp1-4 bpc4 bpc6 triple mutant displayed a pleiotropic phenotype, extreme dwarfism and early flowering, which disclosed synergistic functions of LHP1 and group II plant BPC members. Transcriptome analyses supported this synergy and suggested a possible function in the concerted repression of homeotic genes, probably through histone H3 lysine-27 trimethylation. Hence, our findings suggest striking similarities between animal and plant GAGA-binding factors in the recruitment of PRC1 and PRC2 components to Polycomb-responsive DNA element-like GAGA motifs, which must have evolved through convergent evolution.
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Affiliation(s)
- Andreas Hecker
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Luise H Brand
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Sébastien Peter
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Nathalie Simoncello
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Joachim Kilian
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Klaus Harter
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Valérie Gaudin
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
| | - Dierk Wanke
- Center for Plant Molecular Biology, Plant Physiology, and Biophysical Chemistry, University of Tübingen, 72076 Tuebingen, Germany (A.H., L.H.B., S.P., J.K., K.H., D.W.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1318 AgroParisTech, Institut J.-P. Bourgin, Institut National de la Recherche Agronomique Centre de Versailles-Grignon, F-78026 Versailles, France (N.S., V.G.); andUniversität des Saarlandes, Molekulare Pflanzenbiologie, 66123 Saarbruecken, Germany (D.W.)
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Cubeñas-Potts C, Corces VG. Architectural proteins, transcription, and the three-dimensional organization of the genome. FEBS Lett 2015; 589:2923-30. [PMID: 26008126 DOI: 10.1016/j.febslet.2015.05.025] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/07/2015] [Accepted: 05/09/2015] [Indexed: 12/20/2022]
Abstract
Architectural proteins mediate interactions between distant sequences in the genome. Two well-characterized functions of architectural protein interactions include the tethering of enhancers to promoters and bringing together Polycomb-containing sites to facilitate silencing. The nature of which sequences interact genome-wide appears to be determined by the orientation of the architectural protein binding sites as well as the number and identity of architectural proteins present. Ultimately, long range chromatin interactions result in the formation of loops within the chromatin fiber. In this review, we discuss data suggesting that architectural proteins mediate long range chromatin interactions that both facilitate and hinder neighboring interactions, compartmentalizing the genome into regions of highly interacting chromatin domains.
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Affiliation(s)
- Caelin Cubeñas-Potts
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, USA.
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34
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Caudron-Herger M, Cook PR, Rippe K, Papantonis A. Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories. Nucleic Acids Res 2015; 43:e95. [PMID: 25897132 PMCID: PMC4538806 DOI: 10.1093/nar/gkv390] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/13/2015] [Indexed: 11/21/2022] Open
Abstract
While mapping total and poly-adenylated human transcriptomes has now become routine, characterizing nascent transcripts remains challenging, largely because nascent RNAs have such short half-lives. Here, we describe a simple, fast and cost-effective method to isolate RNA associated with transcription factories, the sites responsible for the majority of nuclear transcription. Following stimulation of human endothelial cells with the pro-inflammatory cytokine TNFα, we isolate and analyse the RNA content of factories by sequencing. Comparison with total, poly(A)+ and chromatin RNA fractions reveals that sequencing of purified factory RNA maps the complete nascent transcriptome; it is rich in intronic unprocessed transcript, as well as long intergenic non-coding (lincRNAs) and enhancer-associated RNAs (eRNAs), micro-RNA precursors and repeat-derived RNAs. Hence, we verify that transcription factories produce most nascent RNA and confer a regulatory role via their association with a set of specifically-retained non-coding transcripts.
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Affiliation(s)
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, UK
| | - Karsten Rippe
- Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, D-69120 Heidelberg, Germany
| | - Argyris Papantonis
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, UK Center for Molecular Medicine, University of Cologne, D-50931 Cologne, Germany
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35
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Razin SV, Gavrilov AA, Ulyanov SV. Transcription-controlling regulatory elements of the eukaryotic genome. Mol Biol 2015. [DOI: 10.1134/s0026893315020119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Abboud N, Morris TM, Hiriart E, Yang H, Bezerra H, Gualazzi MG, Stefanovic S, Guénantin AC, Evans SM, Pucéat M. A cohesin-OCT4 complex mediates Sox enhancers to prime an early embryonic lineage. Nat Commun 2015; 6:6749. [PMID: 25851587 PMCID: PMC5531045 DOI: 10.1038/ncomms7749] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 02/24/2015] [Indexed: 12/20/2022] Open
Abstract
Short- and long-scales intra- and inter-chromosomal interactions are linked to gene transcription, but the molecular events underlying these structures and how they affect cell fate decision during embryonic development are poorly understood. One of the first embryonic cell fate decisions (that is, mesendoderm determination) is driven by the POU factor OCT4, acting in concert with the high-mobility group genes Sox-2 and Sox-17. Here we report a chromatin-remodelling mechanism and enhancer function that mediate cell fate switching. OCT4 alters the higher-order chromatin structure at both Sox-2 and Sox-17 loci. OCT4 titrates out cohesin and switches the Sox-17 enhancer from a locked (within an inter-chromosomal Sox-2 enhancer/CCCTC-binding factor CTCF/cohesin loop) to an active (within an intra-chromosomal Sox-17 promoter/enhancer/cohesin loop) state. SALL4 concomitantly mobilizes the polycomb complexes at the Soxs loci. Thus, OCT4/SALL4-driven cohesin- and polycombs-mediated changes in higher-order chromatin structure mediate instruction of early cell fate in embryonic cells.
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Affiliation(s)
- Nesrine Abboud
- INSERM UMR 633, Genopole Evry, University Paris Descartes, 91000 Evry, Paris, France
| | | | - Emilye Hiriart
- INSERM UMR 633, Genopole Evry, University Paris Descartes, 91000 Evry, Paris, France
- INSERM UMR 910, GMGF, Aix-Marseille University, 13885 Marseille, France
| | - Henry Yang
- Cancer Science Institute, National University of Singapore, Singapore 138672, Singapore
| | - Hudson Bezerra
- INSERM UMR 633, Genopole Evry, University Paris Descartes, 91000 Evry, Paris, France
| | | | - Sonia Stefanovic
- INSERM UMR 633, Genopole Evry, University Paris Descartes, 91000 Evry, Paris, France
- INSERM UMR 910, GMGF, Aix-Marseille University, 13885 Marseille, France
| | - Anne-Claire Guénantin
- INSERM UMR 633, Genopole Evry, University Paris Descartes, 91000 Evry, Paris, France
| | - Sylvia M Evans
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Medecine and Department of Pharmacology, UCSD, La Jolla, California 92093, California, USA
| | - Michel Pucéat
- INSERM UMR 633, Genopole Evry, University Paris Descartes, 91000 Evry, Paris, France
- INSERM UMR 910, GMGF, Aix-Marseille University, 13885 Marseille, France
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Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell 2015; 58:216-31. [PMID: 25818644 DOI: 10.1016/j.molcel.2015.02.023] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/09/2015] [Accepted: 02/19/2015] [Indexed: 12/28/2022]
Abstract
Chromosomes of metazoan organisms are partitioned in the interphase nucleus into discrete topologically associating domains (TADs). Borders between TADs are formed in regions containing active genes and clusters of architectural protein binding sites. The transcription of most genes is repressed after temperature stress in Drosophila. Here we show that temperature stress induces relocalization of architectural proteins from TAD borders to inside TADs, and this is accompanied by a dramatic rearrangement in the 3D organization of the nucleus. TAD border strength declines, allowing for an increase in long-distance inter-TAD interactions. Similar but quantitatively weaker effects are observed upon inhibition of transcription or depletion of individual architectural proteins. Heat shock-induced inter-TAD interactions result in increased contacts among enhancers and promoters of silenced genes, which recruit Pc and form Pc bodies in the nucleolus. These results suggest that the TAD organization of metazoan genomes is plastic and can be reconfigured quickly.
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38
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chromatin-Driven Behavior of Topologically Associating Domains. J Mol Biol 2015; 427:608-25. [DOI: 10.1016/j.jmb.2014.09.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/19/2022]
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40
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Müller-Kuller U, Ackermann M, Kolodziej S, Brendel C, Fritsch J, Lachmann N, Kunkel H, Lausen J, Schambach A, Moritz T, Grez M. A minimal ubiquitous chromatin opening element (UCOE) effectively prevents silencing of juxtaposed heterologous promoters by epigenetic remodeling in multipotent and pluripotent stem cells. Nucleic Acids Res 2015; 43:1577-92. [PMID: 25605798 PMCID: PMC4330381 DOI: 10.1093/nar/gkv019] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Epigenetic silencing of transgene expression represents a major obstacle for the efficient genetic modification of multipotent and pluripotent stem cells. We and others have demonstrated that a 1.5 kb methylation-free CpG island from the human HNRPA2B1-CBX3 housekeeping genes (A2UCOE) effectively prevents transgene silencing and variegation in cell lines, multipotent and pluripotent stem cells, and their differentiated progeny. However, the bidirectional promoter activity of this element may disturb expression of neighboring genes. Furthermore, the epigenetic basis underlying the anti-silencing effect of the UCOE on juxtaposed promoters has been only partially explored. In this study we removed the HNRPA2B1 moiety from the A2UCOE and demonstrate efficient anti-silencing properties also for a minimal 0.7 kb element containing merely the CBX3 promoter. This DNA element largely prevents silencing of viral and tissue-specific promoters in multipotent and pluripotent stem cells. The protective activity of CBX3 was associated with reduced promoter CpG-methylation, decreased levels of repressive and increased levels of active histone marks. Moreover, the anti-silencing effect of CBX3 was locally restricted and when linked to tissue-specific promoters did not activate transcription in off target cells. Thus, CBX3 is a highly attractive element for sustained, tissue-specific and copy-number dependent transgene expression in vitro and in vivo.
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Affiliation(s)
- Uta Müller-Kuller
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Hessen, 60596, Germany
| | - Mania Ackermann
- RG Reprogramming and Gene Therapy, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony, 30625, Germany Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony, 30625, Germany
| | - Stephan Kolodziej
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Hessen, 60596, Germany
| | - Christian Brendel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Hessen, 60596, Germany
| | - Jessica Fritsch
- RG Reprogramming and Gene Therapy, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony, 30625, Germany Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony, 30625, Germany
| | - Nico Lachmann
- RG Reprogramming and Gene Therapy, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony, 30625, Germany Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony, 30625, Germany
| | - Hana Kunkel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Hessen, 60596, Germany
| | - Jörn Lausen
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Hessen, 60596, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony, 30625, Germany Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Moritz
- RG Reprogramming and Gene Therapy, REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Lower Saxony, 30625, Germany Institute of Experimental Hematology, Hannover Medical School, Hannover, Lower Saxony, 30625, Germany
| | - Manuel Grez
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Hessen, 60596, Germany
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Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking. PLoS One 2014; 9:e107765. [PMID: 25247414 PMCID: PMC4172637 DOI: 10.1371/journal.pone.0107765] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/08/2014] [Indexed: 12/27/2022] Open
Abstract
Chromatin insulators of higher eukaryotes functionally divide the genome into active and inactive domains. Furthermore, insulators regulate enhancer/promoter communication, which is evident from the Drosophila bithorax locus in which a multitude of regulatory elements control segment specific gene activity. Centrosomal protein 190 (CP190) is targeted to insulators by CTCF or other insulator DNA-binding factors. Chromatin analyses revealed that insulators are characterized by open and nucleosome depleted regions. Here, we wanted to identify chromatin modification and remodelling factors required for an enhancer blocking function. We used the well-studied Fab-8 insulator of the bithorax locus to apply a genome-wide RNAi screen for factors that contribute to the enhancer blocking function of CTCF and CP190. Among 78 genes required for optimal Fab-8 mediated enhancer blocking, all four components of the NURF complex as well as several subunits of the dREAM complex were most evident. Mass spectrometric analyses of CTCF or CP190 bound proteins as well as immune precipitation confirmed NURF and dREAM binding. Both co-localise with most CP190 binding sites in the genome and chromatin immune precipitation showed that CP190 recruits NURF and dREAM. Nucleosome occupancy and histone H3 binding analyses revealed that CP190 mediated NURF binding results in nucleosomal depletion at CP190 binding sites. Thus, we conclude that CP190 binding to CTCF or to other DNA binding insulator factors mediates recruitment of NURF and dREAM. Furthermore, the enhancer blocking function of insulators is associated with nucleosomal depletion and requires NURF and dREAM.
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Austin JW, Lu P, Majumder P, Ahmed R, Boss JM. STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells. THE JOURNAL OF IMMUNOLOGY 2014; 192:4876-86. [PMID: 24711622 DOI: 10.4049/jimmunol.1302750] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Programmed death-1 (PD-1) is a crucial negative regulator of CD8 T cell development and function, yet the mechanisms that control its expression are not fully understood. Through a nonbiased DNase I hypersensitivity assay, four novel regulatory regions within the Pdcd1 locus were identified. Two of these elements flanked the locus, bound the transcriptional insulator protein CCCTC-binding factor, and interacted with each other, creating a potential regulatory compartmentalization of the locus. In response to T cell activation signaling, NFATc1 bound to two of the novel regions that function as independent regulatory elements. STAT binding sites were identified in these elements as well. In splenic CD8 T cells, TCR-induced PD-1 expression was augmented by IL-6 and IL-12, inducers of STAT3 and STAT4 activity, respectively. IL-6 or IL-12 on its own did not induce PD-1. Importantly, STAT3/4 and distinct chromatin modifications were associated with the novel regulatory regions following cytokine stimulation. The NFATc1/STAT regulatory regions were found to interact with the promoter region of the Pdcd1 gene, providing a mechanism for their action. Together these data add multiple novel distal regulatory regions and pathways to the control of PD-1 expression and provide a molecular mechanism by which proinflammatory cytokines, such as IL-6 or IL-12, can augment PD-1 expression.
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McElroy KA, Kang H, Kuroda MI. Are we there yet? Initial targeting of the Male-Specific Lethal and Polycomb group chromatin complexes in Drosophila. Open Biol 2014; 4:140006. [PMID: 24671948 PMCID: PMC3971409 DOI: 10.1098/rsob.140006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chromatin-binding proteins must navigate the complex nuclear milieu to find their sites of action, and a constellation of protein factors and other properties are likely to influence targeting specificity. Despite considerable progress, the precise rules by which binding specificity is achieved have remained elusive. Here, we consider early targeting events for two groups of chromatin-binding complexes in Drosophila: the Male-Specific Lethal (MSL) and the Polycomb group (PcG) complexes. These two serve as models for understanding targeting, because they have been extensively studied and play vital roles in Drosophila, and their targets have been documented at high resolution. Furthermore, the proteins and biochemical properties of both complexes are largely conserved in multicellular organisms, including humans. While the MSL complex increases gene expression and PcG members repress genes, the two groups share many similarities such as the ability to modify their chromatin environment to create active or repressive domains, respectively. With legacies of in-depth genetic, biochemical and now genomic approaches, the MSL and PcG complexes will continue to provide tractable systems for understanding the recruitment of multiprotein chromatin complexes to their target loci.
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Affiliation(s)
- Kyle A McElroy
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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Maksimenko O, Georgiev P. Mechanisms and proteins involved in long-distance interactions. Front Genet 2014; 5:28. [PMID: 24600469 PMCID: PMC3927085 DOI: 10.3389/fgene.2014.00028] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/25/2014] [Indexed: 12/28/2022] Open
Abstract
Due to advances in genome-wide technologies, consistent distant interactions within chromosomes of higher eukaryotes have been revealed. In particular, it has been shown that enhancers can specifically and directly interact with promoters by looping out intervening sequences, which can be up to several hundred kilobases long. This review is focused on transcription factors that are supposed to be involved in long-range interactions. Available data are in agreement with the model that several known transcription factors and insulator proteins belong to an abundant but poorly studied class of proteins that are responsible for chromosomal architecture.
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Affiliation(s)
- Oksana Maksimenko
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences Moscow, Russia
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Cheutin T, Cavalli G. Polycomb silencing: from linear chromatin domains to 3D chromosome folding. Curr Opin Genet Dev 2014; 25:30-7. [PMID: 24434548 DOI: 10.1016/j.gde.2013.11.016] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/29/2013] [Indexed: 12/22/2022]
Abstract
Polycomb group (PcG) proteins are conserved chromatin factors that regulate key developmental genes. Genome wide studies have shown that PcG proteins and their associated H3K27me3 histone mark cover long genomic domains. PcG proteins and H3K27me3 accumulate in Pc nuclear foci, which are the cellular counterparts of genomic domains silenced by PcG proteins. One explanation for how large genomic domains form nuclear foci may rely on loops occurring between specific elements located within domains. However, recent improvement of the chromosome conformation capture (3C) technology, which allowed monitoring genome wide contacts depicts a more complex picture in which chromosomes are composed of many topologically associating domains (TADs). Chromatin regions marked with H3K27me3 correspond to one class of TADs and PcG proteins participate in long-range interactions of H3K27me3 TADs, whereas insulator proteins seem to be important for separating TADs and may also participate in the regulation of intra TAD architecture. Recent data converge to suggest that this hierarchical organization of chromosome domains plays an important role in genome function during cell proliferation and differentiation.
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Affiliation(s)
- Thierry Cheutin
- Institute of Human Genetics, CNRS UPR 1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS UPR 1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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Benedetti F, Dorier J, Burnier Y, Stasiak A. Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes. Nucleic Acids Res 2013; 42:2848-55. [PMID: 24366878 PMCID: PMC3950722 DOI: 10.1093/nar/gkt1353] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide information about reciprocal spatial proximity of chromosomal loci. Since 2012, it is known that entire chromatin in interphase chromosomes is organized into regions with strongly increased frequency of internal contacts. These regions, with the average size of ∼1 Mb, were named topological domains. More recent studies demonstrated presence of unconstrained supercoiling in interphase chromosomes. Using Brownian dynamics simulations, we show here that by including supercoiling into models of topological domains one can reproduce and thus provide possible explanations of several experimentally observed characteristics of interphase chromosomes, such as their complex contact maps.
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Affiliation(s)
- Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland, Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland and Laboratory of Particle Physics and Cosmology, Institute of Theoretical Physics, Ecole polytechnique fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
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Cecere G, Grishok A. A nuclear perspective on RNAi pathways in metazoans. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1839:223-33. [PMID: 24361586 DOI: 10.1016/j.bbagrm.2013.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 11/27/2013] [Accepted: 11/30/2013] [Indexed: 12/27/2022]
Abstract
The role of RNA interference (RNAi) in post-transcriptional regulation of complementary targets is well known. However, less is known about transcriptional silencing mechanisms mediated by RNAi. Such mechanisms have been characterized in yeast and plants, which suggests that similar RNA silencing mechanisms might operate in animals. A growing amount of experimental evidence indicates that short RNAs and their co-factor Argonaute proteins can regulate many nuclear processes in metazoans. PIWI-interacting RNAs (piRNAs) initiate transcriptional silencing of transposable elements, which leads to heterochromatin formation and/or DNA methylation. In addition, Argonaute proteins and short RNAs directly regulate Pol II transcription and splicing of euchromatic protein-coding genes and also affect genome architecture. Therefore, RNAi pathways can have a profound global impact on the transcriptional programs in cells during animal development. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Germano Cecere
- Department of Biochemistry and Molecular Biophysics, College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Alla Grishok
- Department of Biochemistry and Molecular Biophysics, College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA.
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Matzat LH, Lei EP. Surviving an identity crisis: a revised view of chromatin insulators in the genomics era. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1839:203-14. [PMID: 24189492 DOI: 10.1016/j.bbagrm.2013.10.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
The control of complex, developmentally regulated loci and partitioning of the genome into active and silent domains is in part accomplished through the activity of DNA-protein complexes termed chromatin insulators. Together, the multiple, well-studied classes of insulators in Drosophila melanogaster appear to be generally functionally conserved. In this review, we discuss recent genomic-scale experiments and attempt to reconcile these newer findings in the context of previously defined insulator characteristics based on classical genetic analyses and transgenic approaches. Finally, we discuss the emerging understanding of mechanisms of chromatin insulator regulation. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Leah H Matzat
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elissa P Lei
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Ritland Politz JC, Scalzo D, Groudine M. Something silent this way forms: the functional organization of the repressive nuclear compartment. Annu Rev Cell Dev Biol 2013; 29:241-70. [PMID: 23834025 PMCID: PMC3999972 DOI: 10.1146/annurev-cellbio-101512-122317] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The repressive compartment of the nucleus is comprised primarily of telomeric and centromeric regions, the silent portion of ribosomal RNA genes, the majority of transposable element repeats, and facultatively repressed genes specific to different cell types. This compartment localizes into three main regions: the peripheral heterochromatin, perinucleolar heterochromatin, and pericentromeric heterochromatin. Both chromatin remodeling proteins and transcription of noncoding RNAs are involved in maintenance of repression in these compartments. Global reorganization of the repressive compartment occurs at each cell division, during early development, and during terminal differentiation. Differential action of chromatin remodeling complexes and boundary element looping activities are involved in mediating these organizational changes. We discuss the evidence that heterochromatin formation and compartmentalization may drive nuclear organization.
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Affiliation(s)
| | - David Scalzo
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Mark Groudine
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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