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Isoda T, Morio T, Takagi M. Noncoding RNA transcription at enhancers and genome folding in cancer. Cancer Sci 2019; 110:2328-2336. [PMID: 31228211 PMCID: PMC6676135 DOI: 10.1111/cas.14107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 12/20/2022] Open
Abstract
Changes of nuclear localization of lineage-specific genes from a transcriptionally inert to permissive environment are a crucial step in establishing the identity of a cell. Noncoding RNA transcription-mediated genome folding and activation of target gene expression have been found in a variety of cell types. Noncoding RNA ThymoD (thymocyte differentiation factor) transcription at superenhancers is essential for mouse T-cell lineage commitment. The cessation of ThymoD transcription abolishes transcription-mediated demethylation, recruiting looping factors such as the cohesin complex, CCCTC-binding factor (CTCF), ultimately leading to the phenotype of severe combined immunodeficiency and T-cell leukemia/lymphoma. In this review, we describe the functional role of RNA polymerase II-mediated transcription at enhancers and in genome folding. We also highlight the involvement of faulty activation or suppression of enhancer transcription and enhancer-promoter interaction in cancer development.
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Affiliation(s)
- Takeshi Isoda
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
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2
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Polymer coil-globule phase transition is a universal folding principle of Drosophila epigenetic domains. Epigenetics Chromatin 2019; 12:28. [PMID: 31084607 PMCID: PMC6515630 DOI: 10.1186/s13072-019-0269-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/06/2019] [Indexed: 01/02/2023] Open
Abstract
Background Localized functional domains within chromosomes, known as topologically associating domains (TADs), have been recently highlighted. In Drosophila, TADs are biochemically defined by epigenetic marks, this suggesting that the 3D arrangement may be the “missing link” between epigenetics and gene activity. Recent observations (Boettiger et al. in Nature 529(7586):418–422, 2016) provide access to structural features of these domains with unprecedented resolution thanks to super-resolution experiments. In particular, they give access to the distribution of the radii of gyration for domains of different linear length and associated with different transcriptional activity states: active, inactive or repressed. Intriguingly, the observed scaling laws lack consistent interpretation in polymer physics. Results We develop a new methodology conceived to extract the best information from such super-resolution data by exploiting the whole distribution of gyration radii, and to place these experimental results on a theoretical framework. We show that the experimental data are compatible with the finite-size behavior of a self-attracting polymer. The same generic polymer model leads to quantitative differences between active, inactive and repressed domains. Active domains behave as pure polymer coils, while inactive and repressed domains both lie at the coil–globule crossover. For the first time, the “color-specificity” of both the persistence length and the mean interaction energy are estimated, leading to important differences between epigenetic states. Conclusion These results point toward a crucial role of criticality to enhance the system responsivity, resulting in both energy transitions and structural rearrangements. We get strong indications that epigenetically induced changes in nucleosome–nucleosome interaction can cause chromatin to shift between different activity states. Electronic supplementary material The online version of this article (10.1186/s13072-019-0269-6) contains supplementary material, which is available to authorized users.
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3
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Sano TG, Wada H. Twist-Induced Snapping in a Bent Elastic Rod and Ribbon. PHYSICAL REVIEW LETTERS 2019; 122:114301. [PMID: 30951340 DOI: 10.1103/physrevlett.122.114301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 01/12/2019] [Indexed: 06/09/2023]
Abstract
Snapping of a slender structure is utilized in a wide range of natural and manmade systems, mostly to achieve rapid movement without relying on musclelike elements. Although several mechanisms for elastic energy storage and rapid release have been studied in detail, a general understanding of the approach to design such a kinetic system is a key challenge in mechanics. Here we study a twist-driven buckling and fast flip dynamics of a geometrically constrained ribbon by combining experiments, numerical simulations, and an analytical theory. We identify two distinct types of shape transitions: A narrow ribbon snaps, and a wide ribbon forms a pair of localized helices. We construct a phase diagram and explain the origin of the boundary, which is determined largely by the geometry. We quantify the effects of gravity and clarify the timescale dictating the rapid flipping. Our study reveals the unique role of geometric twist-bend coupling in the fast dynamics of a thin constrained structure, which has implications for a wide range of biophysical and applied physical problems.
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Affiliation(s)
- Tomohiko G Sano
- Department of Physical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hirofumi Wada
- Department of Physical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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4
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Lavelle C. Pack, unpack, bend, twist, pull, push: the physical side of gene expression. Curr Opin Genet Dev 2014; 25:74-84. [PMID: 24576847 DOI: 10.1016/j.gde.2014.01.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 01/03/2014] [Indexed: 12/31/2022]
Abstract
Molecular motors such as polymerases produce physical constraints on DNA and chromatin. Recent techniques, in particular single-molecule micromanipulation, provide estimation of the forces and torques at stake. These biophysical approaches have improved our understanding of chromatin behaviour under physiological physical constraints and should, in conjunction with genome wide and in vivo studies, help to build more realistic mechanistic models of transcription in the context of chromatin. Here, we wish to provide a brief overview of our current knowledge in the field, and emphasize at the same time the importance of DNA supercoiling as a major parameter in gene regulation.
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Affiliation(s)
- Christophe Lavelle
- National Museum of Natural History, Paris, France; CNRS UMR7196, Paris, France; INSERM U1154, Paris, France; Nuclear Architecture and Dynamics, CNRS GDR3536, Paris, France.
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5
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Gilbert N, Allan J. Supercoiling in DNA and chromatin. Curr Opin Genet Dev 2013; 25:15-21. [PMID: 24584092 PMCID: PMC4042020 DOI: 10.1016/j.gde.2013.10.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 01/20/2023]
Abstract
Supercoiling is a fundamental property of DNA and chromatin. It is modulated by polymerase and topoisomerase activities and, through regulated constraint, by DNA/chromatin binding proteins. As a non-covalent and elusive topological modification, supercoiling has proved intractable to research despite being a crucial regulator of nuclear structure and function. Recent studies have improved our understanding of the formation, regulation and organisation of supercoiling domains in vivo, and reinforce the prospect that the propagation of supercoiling can influence local and global chromatin structure. However, to further our understanding the development of new experimental tools and models are required to better dissect the mechanics of this key topological regulator.
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Affiliation(s)
- Nick Gilbert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK.
| | - James Allan
- Institute of Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, UK.
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6
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Marinello J, Chillemi G, Bueno S, Manzo SG, Capranico G. Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation. Nucleic Acids Res 2013; 41:10110-23. [PMID: 23999093 PMCID: PMC3905886 DOI: 10.1093/nar/gkt778] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 12/28/2022] Open
Abstract
DNA Topoisomerase I (Top1) is required to relax DNA supercoils generated by RNA polymerases (RNAPs). Top1 is inhibited with high specificity by camptothecin (CPT), an effective anticancer agent, and by oxidative base damage and ribonucleotides in DNA strands, resulting into Top1-DNA cleavage complexes (Top1ccs). To understand how Top1ccs affect genome stability, we have investigated the global transcriptional response to CPT-induced Top1ccs. Top1ccs trigger an accumulation of antisense RNAPII transcripts specifically at active divergent CpG-island promoters in a replication-independent and Top1-dependent manner. As CPT increases antisense transcript levels in the presence of 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, a transcription inhibitor, Top1ccs likely impair antisense RNA degradation. Time-course data showed a burst of Top1ccs increased by CPT at promoter sites and along transcribed regions, causing a transient block of RNAPII at the promoter. Moreover, cell immunofluorescence analyses showed that Top1ccs induce a transient increase of R-loops specifically at highly transcribed regions such as nucleoli in a Top1-dependent manner. Thus, a specific and highly dynamic transcriptional response to Top1ccs occurs at divergent active CpG-island promoters, which may include a transient stabilization of R-loops. The results clarify molecular features of a response pathway leading to transcription-dependent genome instability and altered transcription regulation.
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Affiliation(s)
- Jessica Marinello
- Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 48, 40126 Bologna, Italy and CASPUR, via dei Tizii 6, Rome 00185, Italy
| | - Giovanni Chillemi
- Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 48, 40126 Bologna, Italy and CASPUR, via dei Tizii 6, Rome 00185, Italy
| | - Susana Bueno
- Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 48, 40126 Bologna, Italy and CASPUR, via dei Tizii 6, Rome 00185, Italy
| | - Stefano G. Manzo
- Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 48, 40126 Bologna, Italy and CASPUR, via dei Tizii 6, Rome 00185, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, University of Bologna, via Irnerio 48, 40126 Bologna, Italy and CASPUR, via dei Tizii 6, Rome 00185, Italy
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7
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Bertozzi D, Marinello J, Manzo SG, Fornari F, Gramantieri L, Capranico G. The Natural Inhibitor of DNA Topoisomerase I, Camptothecin, Modulates HIF-1 Activity by Changing miR Expression Patterns in Human Cancer Cells. Mol Cancer Ther 2013; 13:239-48. [DOI: 10.1158/1535-7163.mct-13-0729] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Abstract
In cells, RNA polymerase (RNAP) must transcribe supercoiled DNA, whose torsional state is constantly changing, but how RNAP deals with DNA supercoiling remains elusive. We report direct measurements of individual Escherichia coli RNAPs as they transcribed supercoiled DNA. We found that a resisting torque slowed RNAP and increased its pause frequency and duration. RNAP was able to generate 11 ± 4 piconewton-nanometers (mean ± standard deviation) of torque before stalling, an amount sufficient to melt DNA of arbitrary sequence and establish RNAP as a more potent torsional motor than previously known. A stalled RNAP was able to resume transcription upon torque relaxation, and transcribing RNAP was resilient to transient torque fluctuations. These results provide a quantitative framework for understanding how dynamic modification of DNA supercoiling regulates transcription.
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Affiliation(s)
- Jie Ma
- Department of Physics-Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
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9
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Barbi M, Mozziconacci J, Wong H, Victor JM. DNA topology in chromosomes: a quantitative survey and its physiological implications. J Math Biol 2012. [PMID: 23179130 DOI: 10.1007/s00285-012-0621-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Using a simple geometric model, we propose a general method for computing the linking number of the DNA embedded in chromatin fibers. The relevance of the method is reviewed through the single molecule experiments that have been performed in vitro with magnetic tweezers. We compute the linking number of the DNA in the manifold conformational states of the nucleosome which have been evidenced in these experiments and discuss the functional dynamics of chromosomes in the light of these manifold states.
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Affiliation(s)
- Maria Barbi
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, and CNRS GDR 3536, Université Pierre et Marie Curie, Case courrier 121, 4 place Jussieu, 75252 , Paris, France,
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10
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Barbi M, Mozziconacci J, Victor JM, Wong H, Lavelle C. On the topology of chromatin fibres. Interface Focus 2012; 2:546-54. [PMID: 24098838 DOI: 10.1098/rsfs.2011.0101] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/10/2012] [Indexed: 11/12/2022] Open
Abstract
The ability of cells to pack, use and duplicate DNA remains one of the most fascinating questions in biology. To understand DNA organization and dynamics, it is important to consider the physical and topological constraints acting on it. In the eukaryotic cell nucleus, DNA is organized by proteins acting as spools on which DNA can be wrapped. These proteins can subsequently interact and form a structure called the chromatin fibre. Using a simple geometric model, we propose a general method for computing topological properties (twist, writhe and linking number) of the DNA embedded in those fibres. The relevance of the method is reviewed through the analysis of magnetic tweezers single molecule experiments that revealed unexpected properties of the chromatin fibre. Possible biological implications of these results are discussed.
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Affiliation(s)
- Maria Barbi
- Laboratoire de Physique Théorique des la Matière condensée, CNRS UMR 7600, Université Pierre et Marie Curie, Case Courrier 121, 4 place Jussieu 75252, Paris Cedex 05, France
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11
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Shahravan SH, Li ITS, Truong K, Shin JA. FRep: A Fluorescent Protein-Based Bioprobe for in Vivo Detection of Protein–DNA Interactions. Anal Chem 2011; 83:9643-50. [DOI: 10.1021/ac2024602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- S. Hesam Shahravan
- Department of Chemical and Physical Sciences, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
| | - Isaac T. S. Li
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
| | - Kevin Truong
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
| | - Jumi A. Shin
- Department of Chemical and Physical Sciences, University of Toronto at Mississauga, Mississauga, Ontario, Canada L5L 1C6
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
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12
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Piatti P, Zeilner A, Lusser A. ATP-dependent chromatin remodeling factors and their roles in affecting nucleosome fiber composition. Int J Mol Sci 2011; 12:6544-65. [PMID: 22072904 PMCID: PMC3210995 DOI: 10.3390/ijms12106544] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 09/20/2011] [Accepted: 09/28/2011] [Indexed: 01/03/2023] Open
Abstract
ATP-dependent chromatin remodeling factors of the SNF2 family are key components of the cellular machineries that shape and regulate chromatin structure and function. Members of this group of proteins have broad and heterogeneous functions ranging from controlling gene activity, facilitating DNA damage repair, promoting homologous recombination to maintaining genomic stability. Several chromatin remodeling factors are critical components of nucleosome assembly processes, and recent reports have identified specific functions of distinct chromatin remodeling factors in the assembly of variant histones into chromatin. In this review we will discuss the specific roles of ATP-dependent chromatin remodeling factors in determining nucleosome composition and, thus, chromatin fiber properties.
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Affiliation(s)
- Paolo Piatti
- Division of Molecular Biology, Innsbruck Medical University, Biocenter, Fritz-Pregl Strasse 3, 6020 Innsbruck, Austria; E-Mails: (P.P.); (A.Z.)
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13
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Lavelle C, Praly E, Bensimon D, Le Cam E, Croquette V. Nucleosome-remodelling machines and other molecular motors observed at the single-molecule level. FEBS J 2011; 278:3596-607. [DOI: 10.1111/j.1742-4658.2011.08280.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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14
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Tsutsui KM, Sano K, Hosoya O, Miyamoto T, Tsutsui K. Nuclear protein LEDGF/p75 recognizes supercoiled DNA by a novel DNA-binding domain. Nucleic Acids Res 2011; 39:5067-81. [PMID: 21345933 PMCID: PMC3130267 DOI: 10.1093/nar/gkr088] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lens epithelium-derived growth factor (LEDGF) or p75 is a co-activator of general transcription and also involved in insertion of human immunodeficiency virus type I (HIV-1) cDNA into host cell genome, which occurs preferentially to active transcription units. These phenomena may share an underlying molecular mechanism in common. We report here that LEDGF/p75 binds negatively supercoiled DNA selectively over unconstrained DNA. We identified a novel DNA-binding domain in the protein and termed it ‘supercoiled DNA-recognition domain’ (SRD). Recombinant protein fragments containing SRD showed a preferential binding to supercoiled DNA in vitro. SRD harbors a characteristic cluster of lysine and glutamic/aspartic acid residues. A polypeptide mimicking the cluster (K9E9K9) also showed this specificity, suggesting that the cluster is an essential element for the supercoil recognition. eGFP-tagged LEDGF/p75 expressed in the nucleus distributed partially in transcriptionally active regions that were identified by immunostaining of methylated histone H3 (H3K4me3) or incorporation of Br-UTP. This pattern of localization was observed with SRD alone but abolished if the protein lacked SRD. Thus, these results imply that LEDGF/p75 guides its binding partners, including HIV-1 integrase, to the active transcription site through recognition of negative supercoils generated around it.
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Affiliation(s)
- Kimiko M. Tsutsui
- Department of Neurogenomics and Department of Genome Dynamics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
- *To whom correspondence should be addressed. Tel: +81 86 235 7096; Fax: +81 86 235 7103;
| | - Kuniaki Sano
- Department of Neurogenomics and Department of Genome Dynamics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Osamu Hosoya
- Department of Neurogenomics and Department of Genome Dynamics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Tadashi Miyamoto
- Department of Neurogenomics and Department of Genome Dynamics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Ken Tsutsui
- Department of Neurogenomics and Department of Genome Dynamics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
- *To whom correspondence should be addressed. Tel: +81 86 235 7096; Fax: +81 86 235 7103;
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15
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Zhang Z, Wang Y, Song T, Gao J, Wu G, Zhang J, Qian X. DNA double helix unwinding triggers transcription block-dependent apoptosis: a semiquantitative probe of the response of ATM, RNAPII, and p53 to two DNA intercalators. Chem Res Toxicol 2010; 22:483-91. [PMID: 19182866 DOI: 10.1021/tx800288v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have previously shown the binding modes of two DNA interacting analogues (1)a {3-(4-methyl-piperazin)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile} and (3)a {3-(3-dimethylamino-propylamino)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile} with the DNA double helix. In this study, we have determined the notably different DNA damage signal pathway elicited by (1)a and (3)a due to the different extents to which they unwind the DNA double helix. First, we have identified that ataxia-telangiectasia-mutated (ATM) protein kinase can respond to DNA double helix unwinding caused by both (1)a and (3)a. In addition, the amount of ATM activation is consistent with the degree to which the DNA double helix was unwound. Consequently, we used (1)a and (3)a to semiquantitatively probe the response of RNA polymerase II (RNAPII) and p53 toward DNA double helix unwinding in vivo. By means of flow cytometry, immunocytochemistry, ChIP, quantitative real-time polymerase chain reaction, and Western blot analyses, we measured the level of p53 and RNAPII phosphorylation, in addition to the dynamics of the RNAPII distribution along the c-Myc gene. These results provided novel evidence for the impact of subtle DNA structural changes on the activity of RNAPII and p53. Moreover, DNA double helix conformational damage-dependent apoptosis was studied for the first time. These results indicated that (1)a can induce transcriptional blockage following a shift of the unphosphorylated IIa form of RNAPII to the phosphorylated IIo form, while (3)a is unable to induce the same effect. Subsequently, p53 accumulation and phosphorylation events occur that lead to apoptosis in the case of (1)a exposure. This suggests that the transcriptional blockage is also correlated to the degree of double helix unwinding. Furthermore, we found that the degree of DNA conformational damage determines whether or not apoptosis occurs through transcriptional blockage. Under our experimental conditions, ATM does not participate in the downstream events even when it has been activated. Thus, p53-mediated apoptosis may be independently triggered by transcriptional blockage.
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Affiliation(s)
- Zhichao Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, People's Republic of China.
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16
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Bécavin C, Barbi M, Victor JM, Lesne A. Transcription within condensed chromatin: Steric hindrance facilitates elongation. Biophys J 2010; 98:824-33. [PMID: 20197036 PMCID: PMC2830436 DOI: 10.1016/j.bpj.2009.10.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Revised: 10/28/2009] [Accepted: 10/29/2009] [Indexed: 11/26/2022] Open
Abstract
During eukaryotic transcription, RNA-polymerase activity generates torsional stress in DNA, having a negative impact on the elongation process. Using our previous studies of chromatin fiber structure and conformational transitions, we suggest that this torsional stress can be alleviated, thanks to a tradeoff between the fiber twist and nucleosome conformational transitions into an activated state named "reversome". Our model enlightens the origin of polymerase pauses, and leads to the counterintuitive conclusion that chromatin-organized compaction might facilitate polymerase progression. Indeed, in a compact and well-structured chromatin loop, steric hindrance between nucleosomes enforces sequential transitions, thus ensuring that the polymerase always meets a permissive nucleosomal state.
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Affiliation(s)
- Christophe Bécavin
- Institut des Hautes Études Scientifiques, Bures-sur-Yvette, France
- Institut de Recherche Interdisciplinaire, Centre National de la Recherche Scientifique, USR 3078, Universités Lille I and II, Villeneuve d'Ascq, France
| | - Maria Barbi
- Laboratoire de Physique Théorique de la Matière Condensée, Centre National de la Recherche Scientifique, UMR 7600, Université Pierre et Marie Curie, Paris, France
| | - Jean-Marc Victor
- Laboratoire de Physique Théorique de la Matière Condensée, Centre National de la Recherche Scientifique, UMR 7600, Université Pierre et Marie Curie, Paris, France
| | - Annick Lesne
- Institut des Hautes Études Scientifiques, Bures-sur-Yvette, France
- Laboratoire de Physique Théorique de la Matière Condensée, Centre National de la Recherche Scientifique, UMR 7600, Université Pierre et Marie Curie, Paris, France
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Wong H, Winn PJ, Mozziconacci J. A molecular model of chromatin organisation and transcription:how a multi-RNA polymerase II machine transcribes and remodels the β-globin locus during development. Bioessays 2009; 31:1357-66. [DOI: 10.1002/bies.200900062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Lavelle C. Forces and torques in the nucleus: chromatin under mechanical constraints. Biochem Cell Biol 2009; 87:307-22. [PMID: 19234543 DOI: 10.1139/o08-123] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genomic DNA in eukaryotic cells is organized in discrete chromosome territories, each consisting of a single huge hierarchically supercoiled nucleosomal fiber. Through dynamic changes in structure, resulting from chemical modifications and mechanical constraints imposed by numerous factors in vivo, chromatin plays a critical role in the regulation of DNA metabolism processes, including replication and transcription. Indeed, DNA-translocating enzymes, such as polymerases, produce physical constraints that chromatin has to overcome. Recent techniques, in particular single-molecule micromanipulation, have allowed precise quantization of forces and torques at work in the nucleus and have greatly improved our understanding of chromatin behavior under physiological mechanical constraints. These new biophysical approaches should enable us to build realistic mechanistic models and progressively specify the ad hoc and hazy "because of chromatin structure" argument often used to interpret experimental studies of biological function in the context of chromatin.
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Stricker SH, Steenpass L, Pauler FM, Santoro F, Latos PA, Huang R, Koerner MV, Sloane MA, Warczok KE, Barlow DP. Silencing and transcriptional properties of the imprinted Airn ncRNA are independent of the endogenous promoter. EMBO J 2008; 27:3116-28. [PMID: 19008856 DOI: 10.1038/emboj.2008.239] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 10/17/2008] [Indexed: 01/09/2023] Open
Abstract
The Airn macro ncRNA is the master regulator of imprinted expression in the Igf2r imprinted gene cluster where it silences three flanking genes in cis. Airn transcription shows unusual features normally viewed as promoter specific, such as impaired post-transcriptional processing and a macro size. The Airn transcript is 108 kb long, predominantly unspliced and nuclear localized, with only a minority being variably spliced and exported. Here, we show by deletion of the Airn ncRNA promoter and replacement with a constitutive strong or weak promoter that splicing suppression and termination, as well as silencing activity, are maintained by strong Airn expression from an exogenous promoter. This indicates that all functional regions are located within the Airn transcript. DNA methylation of the maternal imprint control element (ICE) restricts Airn expression to the paternal allele and we also show that a strong active promoter is required to maintain the unmethylated state of the paternal ICE. Thus, Airn expression not only induces silencing of flanking mRNA genes but also protects the paternal copy of the ICE from de novo methylation.
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Affiliation(s)
- Stefan H Stricker
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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Dupaigne P, Lavelle C, Justome A, Lafosse S, Mirambeau G, Lipinski M, Piétrement O, Le Cam E. Rad51 polymerization reveals a new chromatin remodeling mechanism. PLoS One 2008; 3:e3643. [PMID: 18982066 PMCID: PMC2574414 DOI: 10.1371/journal.pone.0003643] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 10/11/2008] [Indexed: 12/26/2022] Open
Abstract
Rad51 protein is a well known protagonist of homologous recombination in eukaryotic cells. Rad51 polymerization on single-stranded DNA and its role in presynaptic filament formation have been extensively documented. Rad51 polymerizes also on double-stranded DNA but the significance of this filament formation remains unclear. We explored the behavior of Saccharomyces cerevisiae Rad51 on dsDNA and the influence of nucleosomes on Rad51 polymerization mechanism to investigate its putative role in chromatin accessibility to recombination machinery. We combined biochemical approaches, transmission electron microscopy (TEM) and atomic force microscopy (AFM) for analysis of the effects of the Rad51 filament on chromatinized templates. Quantitative analyses clearly demonstrated the occurrence of chromatin remodeling during nucleoprotein filament formation. During Rad51 polymerization, recombinase proteins moved all the nucleosomal arrays in front of the progressing filament. This polymerization process had a powerful remodeling effect, as Rad51 destabilized the nucleosomes along considerable stretches of DNA. Similar behavior was observed with RecA. Thus, recombinase polymerization is a powerful mechanism of chromatin remodeling. These remarkable features open up new possibilities for understanding DNA recombination and reveal new types of ATP-dependent chromatin dynamics.
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Affiliation(s)
- Pauline Dupaigne
- CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, France
- Univ. Paris-Sud, Villejuif, France
| | - Christophe Lavelle
- CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, France
- Univ. Paris-Sud, Villejuif, France
| | - Anthony Justome
- CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, France
- Univ. Paris-Sud, Villejuif, France
| | - Sophie Lafosse
- CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, France
- Univ. Paris-Sud, Villejuif, France
| | - Gilles Mirambeau
- CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, France
- Division de Biochimie, UFR des Sciences de la Vie, Univ. Pierre et Marie Curie, Paris, France
| | - Marc Lipinski
- CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, France
- Univ. Paris-Sud, Villejuif, France
| | - Olivier Piétrement
- CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, France
- Univ. Paris-Sud, Villejuif, France
- * E-mail: (OP); (ELC)
| | - Eric Le Cam
- CNRS, Laboratoire de Microscopie Moléculaire et Cellulaire, UMR 8126 Interactions Moléculaires et Cancer, Institut de cancérologie Gustave Roussy, Villejuif, France
- Univ. Paris-Sud, Villejuif, France
- * E-mail: (OP); (ELC)
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21
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Lavelle C. DNA torsional stress propagates through chromatin fiber and participates in transcriptional regulation. Nat Struct Mol Biol 2008; 15:123-5. [DOI: 10.1038/nsmb0208-123] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lavelle C, Salles B, Wiesmüller L. DNA repair, damage signaling and carcinogenesis. DNA Repair (Amst) 2008; 7:670-80. [PMID: 18221920 DOI: 10.1016/j.dnarep.2007.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2007] [Indexed: 12/14/2022]
Abstract
The First joint meeting of the German DGDR (German Society for Research on DNA Repair) and the French SFTG (French Society of Genotoxicology) on DNA Repair was held in Toulouse, France, from September 15 to 19, 2007. It was organized by Lisa Wiesmüller and Bernard Salles together with the scientific committee consisting of Gilbert de Murcia, Jean-Marc Egly, Frank Grosse, Karl-Peter Hopfner, Georges Iliakis, Bernd Kaina, Markus Löbrich, Bernard Lopez, Daniel Marzin and Alain Sarasin. This report summarizes information presented by the speakers (invited lectures and oral communications) during the seven plenary sessions, which include (1) excision repair, (2) DNA repair and carcinogenesis, (3) double-strand break repair, (4) replication in repair and lesion bypass, (5) cellular responses to genotoxic stress, (6) DNA repair machinery within the chromatin context and (7) genotoxicology and testing. A total of 23 plenary lectures, 32 oral communications and 66 posters were presented in this rather intense 4 days meeting, which stimulated extensive discussions and highly interdisciplinary scientific exchanges among the approximately 250 participants.
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Armstrong JA. Negotiating the nucleosome: factors that allow RNA polymerase II to elongate through chromatin. Biochem Cell Biol 2008; 85:426-34. [PMID: 17713578 DOI: 10.1139/o07-054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Initiation by RNA polymerase II (Pol II) involves a host of enzymes, and the process of elongation appears similarly complex. Transcriptional elongation through chromatin requires the coordinated efforts of Pol II and its associated transcription factors: C-terminal domain kinases, elongation complexes, chromatin-modifying enzymes, chromatin remodeling factors, histone chaperones (nucleosome assembly factors), and histone variants. This review examines the following: (i) the consequences of the encounter between elongating Pol II and a nucleosome, and (ii) chromatin remodeling factors and nucleosome assembly factors that have recently been identified as important for the elongation stage of transcription.
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Affiliation(s)
- Jennifer A Armstrong
- Joint Science Department, The Claremont Colleges, 925 N. Mills Avenue, Claremont, CA 91711, USA.
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