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Geng Y, Bohrer CH, Yehya N, Hendrix H, Shachaf L, Liu J, Xiao J, Roberts E. A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation. PLoS Comput Biol 2022; 18:e1009788. [PMID: 36121892 PMCID: PMC9522292 DOI: 10.1371/journal.pcbi.1009788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 09/29/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
In Escherichia coli, translocation of RNA polymerase (RNAP) during transcription introduces supercoiling to DNA, which influences the initiation and elongation behaviors of RNAP. To quantify the role of supercoiling in transcription regulation, we developed a spatially resolved supercoiling model of transcription. The integrated model describes how RNAP activity feeds back with the local DNA supercoiling and how this mechanochemical feedback controls transcription, subject to topoisomerase activities and stochastic topological domain formation. This model establishes that transcription-induced supercoiling mediates the cooperation of co-transcribing RNAP molecules in highly expressed genes, and this cooperation is achieved under moderate supercoiling diffusion and high topoisomerase unbinding rates. It predicts that a topological domain could serve as a transcription regulator, generating substantial transcriptional noise. It also shows the relative orientation of two closely arranged genes plays an important role in regulating their transcription. The model provides a quantitative platform for investigating how genome organization impacts transcription.
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Affiliation(s)
- Yuncong Geng
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | - Christopher Herrick Bohrer
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Nicolás Yehya
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Hunter Hendrix
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Lior Shachaf
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jian Liu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Elijah Roberts
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
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2
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Abstract
The compaction of linear DNA into micrometer-sized nuclear boundaries involves the establishment of specific three-dimensional (3D) DNA structures complexed with histone proteins that form chromatin. The resulting structures modulate essential nuclear processes such as transcription, replication, and repair to facilitate or impede their multi-step progression and these contribute to dynamic modification of the 3D-genome organization. It is generally accepted that protein–protein and protein–DNA interactions form the basis of 3D-genome organization. However, the constant generation of mechanical forces, torques, and other stresses produced by various proteins translocating along DNA could be playing a larger role in genome organization than currently appreciated. Clearly, a thorough understanding of the mechanical determinants imposed by DNA transactions on the 3D organization of the genome is required. We provide here an overview of our current knowledge and highlight the importance of DNA and chromatin mechanics in gene expression.
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Affiliation(s)
- Rajiv Kumar Jha
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - Fedor Kouzine
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
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3
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Ng GYQ, Yun-An L, Sobey CG, Dheen T, Fann DYW, Arumugam TV. Epigenetic regulation of inflammation in stroke. Ther Adv Neurol Disord 2018; 11:1756286418771815. [PMID: 29774056 PMCID: PMC5949939 DOI: 10.1177/1756286418771815] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 03/29/2018] [Indexed: 12/30/2022] Open
Abstract
Despite extensive research, treatments for clinical stroke are still limited only to the administration of tissue plasminogen activator and the recent introduction of mechanical thrombectomy, which can be used in only a limited proportion of patients due to time constraints. A plethora of inflammatory events occur during stroke, arising in part due to the body's immune response to brain injury. Neuroinflammation contributes significantly to neuronal cell death and the development of functional impairment and death in stroke patients. Therefore, elucidating the molecular and cellular mechanisms underlying inflammatory damage following stroke injury will be essential for the development of useful therapies. Research findings increasingly point to the likelihood that epigenetic mechanisms play a role in the pathophysiology of stroke. Epigenetics involves the differential regulation of gene expression, including those involved in brain inflammation and remodelling after stroke. Hence, it is conceivable that epigenetic mechanisms may contribute to differential interindividual vulnerability and injury responses to cerebral ischaemia. In this review, we summarize recent findings on the emerging role of epigenetics in the regulation of neuroinflammation in stroke. We also discuss potential epigenetic targets that may be assessed for the development of stroke therapies.
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Affiliation(s)
- Gavin Yong-Quan Ng
- Department of Physiology, Yong Loo Lin School Medicine, National University of Singapore, Singapore
| | - Lim Yun-An
- Department of Physiology, Yong Loo Lin School Medicine, National University of Singapore, Singapore
| | - Christopher G. Sobey
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, Australia
| | - Thameem Dheen
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - David Yang-Wei Fann
- Department of Physiology, Yong Loo Lin School Medicine, National University of Singapore, Singapore
| | - Thiruma V. Arumugam
- Department of Physiology, Yong Loo Lin School Medicine, National University of Singapore, Medical Drive, MD9, Singapore School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore
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4
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Lesne A, Victor JM, Bertrand E, Basyuk E, Barbi M. The Role of Supercoiling in the Motor Activity of RNA Polymerases. Methods Mol Biol 2018; 1805:215-232. [PMID: 29971720 DOI: 10.1007/978-1-4939-8556-2_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA polymerase (RNAP) is, in its elongation phase, an emblematic example of a molecular motor whose activity is highly sensitive to DNA supercoiling. After a review of DNA supercoiling basic features, we discuss how supercoiling controls polymerase velocity, while being itself modified by polymerase activity. This coupling is supported by single-molecule measurements. Physical modeling allows us to describe quantitatively how supercoiling and torsional constraints mediate a mechanical coupling between adjacent polymerases. On this basis, we obtain a description that may explain the existence and functioning of RNAP convoys.
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Affiliation(s)
- Annick Lesne
- Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), UMR 7600 CNRS, Sorbonne Université, Paris, France.,Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, Montpellier, France.,Université de Montpellier, Montpellier, France.,GDR 3536 CNRS, Sorbonne Université, Paris, France
| | - Jean-Marc Victor
- Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), UMR 7600 CNRS, Sorbonne Université, Paris, France. .,Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, Montpellier, France. .,Université de Montpellier, Montpellier, France. .,GDR 3536 CNRS, Sorbonne Université, Paris, France.
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, Montpellier, France.,Université de Montpellier, Montpellier, France
| | - Maria Barbi
- Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), UMR 7600 CNRS, Sorbonne Université, Paris, France.,GDR 3536 CNRS, Sorbonne Université, Paris, France
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5
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Abstract
The twin-supercoiled-domain model describes how transcription can drive DNA supercoiling, and how DNA supercoiling, in turn plays an important role in regulating gene transcription. In vivo and in vitro experiments have disclosed many details of the complex interactions in this relationship, and recently new insights have been gained with the help of genome-wide DNA supercoiling mapping techniques and single molecule methods. This review summarizes the general mechanisms of the interplay between DNA supercoiling and transcription, considers the biological implications, and focuses on recent important discoveries and technical advances in this field. We highlight the significant impact of DNA supercoiling in transcription, but also more broadly in all processes operating on DNA.
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Affiliation(s)
- Jie Ma
- School of Physics ; State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-Sen University, Guangzhou, 510275, PRC
| | - Michelle D Wang
- Department of Physics - Laboratory of Atomic and Solid State Physics ; Howard Hughes Medical Institute, Cornell University, Ithaca, NY, 14853, USA
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6
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Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues. Methods 2016; 98:134-142. [DOI: 10.1016/j.ymeth.2015.11.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 11/15/2015] [Accepted: 11/19/2015] [Indexed: 11/23/2022] Open
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7
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Nam GM, Arya G. Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes. Phys Rev E 2016; 93:032406. [PMID: 27078389 DOI: 10.1103/physreve.93.032406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 06/05/2023]
Abstract
The nucleosome represents the basic unit of eukaryotic genome organization, and its conformational fluctuations play a crucial role in various cellular processes. Here we provide insights into the flipping transition of a nucleosome by computing its free-energy landscape as a function of the linking number and nucleosome orientation using the density-of-states Monte Carlo approach. To investigate how the energy landscape is affected by the presence of neighboring nucleosomes in a chromatin fiber, we also compute the free-energy landscape for a dinucleosome array. We find that the mononucleosome is bistable between conformations with negatively and positively crossed linkers while the conformation with open linkers appears as a transition state. The dinucleosome exhibits a markedly different energy landscape in which the conformation with open linkers populates not only the transition state but also the global minimum. This enhanced stability of the open state is attributed to increased rotational flexibility of nucleosomes arising from their mechanical coupling with neighboring nucleosomes. Our results provide a possible mechanism by which chromatin may enhance the accessibility of its DNA and facilitate the propagation and mitigation of DNA torsional stresses.
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Affiliation(s)
- Gi-Moon Nam
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, USA
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0448, USA
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8
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Norouzi D, Katebi A, Cui F, Zhurkin VB. Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription. AIMS BIOPHYSICS 2015; 2:613-629. [PMID: 28133628 PMCID: PMC5271602 DOI: 10.3934/biophy.2015.4.613] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To tackle this problem, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10–70 bp (nucleosome repeat length NRL = 157–217 bp). In our model, the energy of a fiber is a sum of the elastic energy of the linker DNA, steric repulsion, electrostatics, and the H4 tail-acidic patch interaction between two stacked nucleosomes. We found two families of energetically feasible conformations of the fibers—one observed earlier, and the other novel. The fibers from the two families are characterized by different DNA linking numbers—that is, they are topologically different. Remarkably, the optimal geometry of a fiber and its topology depend on the linker length: the fibers with linkers L = 10n and 10n + 5 bp have DNA linking numbers per nucleosome ΔLk ≈ −1.5 and −1.0, respectively. In other words, the level of DNA supercoiling is directly related to the length of the inter-nucleosome linker in the chromatin fiber (and therefore, to NRL). We hypothesize that this topological polymorphism of chromatin fibers may play a role in the process of transcription, which is known to generate different levels of DNA supercoiling upstream and downstream from RNA polymerase. A genome-wide analysis of the NRL distribution in active and silent yeast genes yielded results consistent with this assumption.
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Affiliation(s)
- Davood Norouzi
- Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA
| | - Ataur Katebi
- Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA
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9
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Lesne A, Foray N, Cathala G, Forné T, Wong H, Victor JM. Chromatin fiber allostery and the epigenetic code. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:064114. [PMID: 25563208 DOI: 10.1088/0953-8984/27/6/064114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The notion of allostery introduced for proteins about fifty years ago has been extended since then to DNA allostery, where a locally triggered DNA structural transition remotely controls other DNA-binding events. We further extend this notion and propose that chromatin fiber allosteric transitions, induced by histone-tail covalent modifications, may play a key role in transcriptional regulation. We present an integrated scenario articulating allosteric mechanisms at different scales: allosteric transitions of the condensed chromatin fiber induced by histone-tail acetylation modify the mechanical constraints experienced by the embedded DNA, thus possibly controlling DNA-binding of allosteric transcription factors or further allosteric mechanisms at the linker DNA level. At a higher scale, different epigenetic constraints delineate different statistically dominant subsets of accessible chromatin fiber conformations, which each favors the assembly of dedicated regulatory complexes, as detailed on the emblematic example of the mouse Igf2-H19 gene locus and its parental imprinting. This physical view offers a mechanistic and spatially structured explanation of the observed correlation between transcriptional activity and histone modifications. The evolutionary origin of allosteric control supports to speak of an 'epigenetic code', by which events involved in transcriptional regulation are encoded in histone modifications in a context-dependent way.
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Affiliation(s)
- Annick Lesne
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, UPMC Université Paris 06, Sorbonne Universités, F-75005, Paris, France. Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535, Université de Montpellier, F-34293, Montpellier, France. CNRS GDR 3536, UPMC Université Paris 06, F-75005, Paris, France
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10
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Abstract
The double helical structure of DNA lends itself to topological constraints. Many DNA-based processes alter the topological state of DNA, generating torsional stress, which is efficiently relieved by topoisomerases. Maintaining this topological balance is crucial to cell survival, as excessive torsional strain risks DNA damage. Here, we review the mechanisms that generate and modulate DNA torsion within the cell. In particular, we discuss how transcription-generated torsional stress affects Pol II kinetics and chromatin dynamics, highlighting an emerging role of DNA torsion as a feedback mediator of torsion-generating processes.
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Affiliation(s)
- Sheila S Teves
- Molecular and Cell Biology; University of California, Berkeley; Berkeley, CA USA
| | - Steven Henikoff
- Basic Sciences Division; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Howard Hughes Medical Institute; Seattle, WA USA
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11
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Transcription-generated torsional stress destabilizes nucleosomes. Nat Struct Mol Biol 2013; 21:88-94. [PMID: 24317489 PMCID: PMC3947361 DOI: 10.1038/nsmb.2723] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 10/30/2013] [Indexed: 01/03/2023]
Abstract
As RNA polymerase II (Pol II) transcribes a gene, it encounters an array of well-ordered nucleosomes. How it traverses through this array in vivo remains unresolved. One model proposes that torsional stress generated during transcription destabilizes nucleosomes ahead of Pol II. Here, we describe a method for high-resolution mapping of underwound DNA, using next-generation sequencing, and show that torsion is correlated with gene expression in Drosophila melanogaster cells. Accumulation of torsional stress, through topoisomerase inhibition, results in increased Pol II at transcription start sites. Whereas topoisomerase I inhibition results in increased nascent RNA transcripts, topoisomerase II inhibition causes little change. Despite the different effects on Pol II elongation, topoisomerase inhibition results in increased nucleosome turnover and salt solubility within gene bodies, thus suggesting that the elongation-independent effects of torsional stress on nucleosome dynamics contributes to the destabilization of nucleosomes.
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12
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Abstract
Host-pathogen interactions provide a fascinating example of two or more active genomes directly exerting mutual influence upon each other. These encounters can lead to multiple outcomes from symbiotic homeostasis to mutual annihilation, undergo multiple cycles of latency and lysogeny, and lead to coevolution of the interacting genomes. Such systems pose numerous challenges but also some advantages to modeling, especially in terms of functional, mathematical genome representations. The main challenges for the modeling process start with the conceptual definition of a genome for instance in the case of host-integrated viral genomes. Furthermore, hardly understood influences of the activity of either genome on the other(s) via direct and indirect mechanisms amplify the needs for a coherent description of genome activity. Finally, genetic and local environmental heterogeneities in both the host's cellular and the pathogen populations need to be considered in multiscale modeling efforts. We will review here two prominent examples of host-pathogen interactions at the genome level, discuss the current modeling efforts and their shortcomings, and explore novel ideas of representing active genomes which promise being particularly adapted to dealing with the modeling challenges posed by host-pathogen interactions.
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Affiliation(s)
- Arndt G Benecke
- Centre National de la Recherche Scientifique, Institut des Hautes Études Scientifiques, 35 route de Chartres, 91440, Bures sur Yvette, France.
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13
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Abstract
It is argued that multiscale approaches are necessary for an explanatory modeling of biological systems. A first step, besides common to the multiscale modeling of physical and living systems, is a bottom-up integration based on the notions of effective parameters and minimal models. Top-down effects can be accounted for in terms of effective constraints and inputs. Biological systems are essentially characterized by an entanglement of bottom-up and top-down influences following from their evolutionary history. A self-consistent multiscale scheme is proposed to capture the ensuing circular causality. Its differences with standard mean-field self-consistent equations and slow-fast decompositions are discussed. As such, this scheme offers a way to unravel the multilevel architecture of living systems and their regulation. Two examples, genome functions and biofilms, are detailed.
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Affiliation(s)
- Annick Lesne
- CNRS UMR 7600, Université Pierre et Marie Curie-Paris 6, 4 place Jussieu, 75252 Paris Cedex 05, France.
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14
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Teves SS, Henikoff S. The heat shock response: A case study of chromatin dynamics in gene regulation. Biochem Cell Biol 2013; 91:42-8. [DOI: 10.1139/bcb-2012-0075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Recent studies in transcriptional regulation using the Drosophila heat shock response system have elucidated many of the dynamic regulatory processes that govern transcriptional activation and repression. The classic view that the control of gene expression occurs at the point of RNA polymerase II (Pol II) recruitment is now giving way to a more complex outlook of gene regulation. Promoter chromatin dynamics coordinate with transcription factor binding to maintain the promoters of active genes accessible. For a large number of genes, the rate-limiting step in Pol II progression occurs during its initial elongation, where Pol II transcribes 30–50 bp and pauses for further signals. These paused genes have unique genic chromatin architecture and dynamics compared with genes where Pol II recruitment is rate limiting for expression. Further elongation of Pol II along the gene causes nucleosome turnover, a continuous process of eviction and replacement, which suggests a potential mechanism for Pol II transit along a nucleosomal template. In this review, we highlight recent insights into transcription regulation of the heat shock response and discuss how the dynamic regulatory processes involved at each transcriptional stage help to generate faithful yet highly responsive gene expression.
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Affiliation(s)
- Sheila S. Teves
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
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15
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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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16
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One step back before moving forward: regulation of transcription elongation by arrest and backtracking. FEBS Lett 2012; 586:2820-5. [PMID: 22819814 DOI: 10.1016/j.febslet.2012.07.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 07/09/2012] [Accepted: 07/10/2012] [Indexed: 12/14/2022]
Abstract
RNA polymerase II backtracking is a well-known phenomenon, but its involvement in gene regulation is yet to be addressed. Structural studies into the backtracked complex, new reactivation mechanisms and genome-wide approaches are shedding some light on this interesting aspect of gene transcription. In this review, we briefly summarise these new findings, comment about some results recently obtained in our laboratory, and propose a new model for the influence of the chromatin context on RNA polymerase II backtracking.
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17
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Lesne A, Bécavin C, Victor JM. The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing. Phys Biol 2012; 9:013001. [PMID: 22314931 DOI: 10.1088/1478-3975/9/1/013001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity.
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Affiliation(s)
- Annick Lesne
- CNRS UMR 7600, Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France.
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18
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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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19
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Towards a molecular view of transcriptional control. Curr Opin Struct Biol 2012; 22:160-7. [PMID: 22296921 DOI: 10.1016/j.sbi.2012.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 01/06/2012] [Accepted: 01/09/2012] [Indexed: 11/21/2022]
Abstract
The accumulation of experimental data over recent years has fueled theoretical work on how transcription factors (TFs) search for and recognise their DNA target sites, how they interact with one another, or with other DNA-binding proteins, and how they cope with the compaction of DNA within bacterial nucleoids or within eukaryotic chromatin. Many models have been built to study the kinetic, thermodynamic and mechanistic aspects of these questions. In some cases they have resulted in a relatively clear consensus view, but a number of questions remain controversial. We present an overview of recent work, with an emphasis on models that provide, or can inspire, a better understanding of transcriptional control at a detailed molecular level.
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20
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Killian JL, Li M, Sheinin MY, Wang MD. Recent advances in single molecule studies of nucleosomes. Curr Opin Struct Biol 2011; 22:80-7. [PMID: 22172540 DOI: 10.1016/j.sbi.2011.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/07/2011] [Accepted: 11/09/2011] [Indexed: 01/14/2023]
Abstract
As the fundamental packing units of DNA in eukaryotes, nucleosomes play a central role in governing DNA accessibility in a variety of cellular processes. Our understanding of the mechanisms underlying this complex regulation has been aided by unique structural and dynamic perspectives offered by single molecule techniques. Recent years have witnessed remarkable advances achieved using these techniques, including the generation of a detailed histone-DNA energy landscape, elucidation of nucleosome disassembly processes, and real-time monitoring of molecular motors interacting with nucleosomes. These and other highlights of single molecule nucleosome studies will be discussed in this review.
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Affiliation(s)
- Jessica L Killian
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
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Böhm V, Hieb AR, Andrews AJ, Gansen A, Rocker A, Tóth K, Luger K, Langowski J. Nucleosome accessibility governed by the dimer/tetramer interface. Nucleic Acids Res 2010; 39:3093-102. [PMID: 21177647 PMCID: PMC3082900 DOI: 10.1093/nar/gkq1279] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nucleosomes are multi-component macromolecular assemblies which present a formidable obstacle to enzymatic activities that require access to the DNA, e.g. DNA and RNA polymerases. The mechanism and pathway(s) by which nucleosomes disassemble to allow DNA access are not well understood. Here we present evidence from single molecule FRET experiments for a previously uncharacterized intermediate structural state before H2A–H2B dimer release, which is characterized by an increased distance between H2B and the nucleosomal dyad. This suggests that the first step in nucleosome disassembly is the opening of the (H3–H4)2 tetramer/(H2A–H2B) dimer interface, followed by H2A–H2B dimer release from the DNA and, lastly, (H3–H4)2 tetramer removal. We estimate that the open intermediate state is populated at 0.2–3% under physiological conditions. This finding could have significant in vivo implications for factor-mediated histone removal and exchange, as well as for regulating DNA accessibility to the transcription and replication machinery.
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Affiliation(s)
- Vera Böhm
- Abteilung Biophysik der Makromoleküle, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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