101
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Abstract
DNA replication in a human cell involves hundreds of proteins that copy the DNA accurately and completely each cell division cycle. In addition to the core DNA copying machine (the replisome), accessory proteins work to respond to replication stress, correct errors, and repackage the DNA into appropriate chromatin structures. New proteomic tools have been invented in the past few years to facilitate the purification, identification, and quantification of the replication, chromatin maturation, and replication stress response machineries. These tools, including iPOND (isolation of proteins on nascent DNA) and NCC (nascent chromatin capture), have yielded discoveries of new proteins involved in these processes and insights into the dynamic regulatory processes ensuring genome and chromatin integrity. In this review, I will introduce these experimental approaches and examine how they have been utilized to define the replication fork proteome.
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Affiliation(s)
- David Cortez
- Vanderbilt University School of Medicine, Nashville, TN, United States.
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102
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Facilitated dissociation of transcription factors from single DNA binding sites. Proc Natl Acad Sci U S A 2017; 114:E3251-E3257. [PMID: 28364020 DOI: 10.1073/pnas.1701884114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits that TF off rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key Escherichia coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate [Formula: see text], establishing that FD of Fis occurs at the single-binding site level, and we find that the off rate saturates at large Fis concentrations in solution. Although spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that FD depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF with structure that differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those that we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap.
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103
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Abstract
Steady-state gene expression across the cell cycle has been studied extensively. However, transcriptional gene regulation and the dynamics of histone modification at different cell-cycle stages are largely unknown. By applying a combination of global nuclear run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and histone-modification Chip sequencing (ChIP-seq), we depicted a comprehensive transcriptional landscape at the G0/G1, G1/S, and M phases of breast cancer MCF-7 cells. Importantly, GRO-seq and RNA-seq analysis identified different cell-cycle-regulated genes, suggesting a lag between transcription and steady-state expression during the cell cycle. Interestingly, we identified genes actively transcribed at early M phase that are longer in length and have low expression and are accompanied by a global increase in active histone 3 lysine 4 methylation (H3K4me2) and histone 3 lysine 27 acetylation (H3K27ac) modifications. In addition, we identified 2,440 cell-cycle-regulated enhancer RNAs (eRNAs) that are strongly associated with differential active transcription but not with stable expression levels across the cell cycle. Motif analysis of dynamic eRNAs predicted Kruppel-like factor 4 (KLF4) as a key regulator of G1/S transition, and this identification was validated experimentally. Taken together, our combined analysis characterized the transcriptional and histone-modification profile of the human cell cycle and identified dynamic transcriptional signatures across the cell cycle.
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104
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Bonifer C, Cockerill PN. Chromatin priming of genes in development: Concepts, mechanisms and consequences. Exp Hematol 2017; 49:1-8. [PMID: 28185904 DOI: 10.1016/j.exphem.2017.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/19/2017] [Accepted: 01/21/2017] [Indexed: 01/06/2023]
Abstract
During ontogeny, cells progress through multiple alternate differentiation states by activating distinct gene regulatory networks. In this review, we highlight the important role of chromatin priming in facilitating gene activation during lineage specification and in maintaining an epigenetic memory of previous gene activation. We show that chromatin priming is part of a hugely diverse repertoire of regulatory mechanisms that genes use to ensure that they are expressed at the correct time, in the correct cell type, and at the correct level, but also that they react to signals. We also emphasize how increasing our knowledge of these principles could inform our understanding of developmental failure and disease.
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Affiliation(s)
- Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK.
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK.
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105
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Birnbaum KD, Roudier F. Epigenetic memory and cell fate reprogramming in plants. ACTA ACUST UNITED AC 2017; 4:15-20. [PMID: 28316791 PMCID: PMC5350078 DOI: 10.1002/reg2.73] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 12/30/2022]
Abstract
Plants have a high intrinsic capacity to regenerate from adult tissues, with the ability to reprogram adult cell fates. In contrast, epigenetic mechanisms have the potential to stabilize cell identity and maintain tissue organization. The question is whether epigenetic memory creates a barrier to reprogramming that needs to be erased or circumvented in plant regeneration. Early evidence suggests that, while chromatin dynamics impact gene expression in the meristem, a lasting constraint on cell fate is not established until late stages of plant cell differentiation. It is not yet clear whether the plasticity of plant cells arises from the ability of cells to erase identity memory or to deploy cells that may exhibit cellular specialization but still lack an epigenetic restriction on cell fate alteration.
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Affiliation(s)
- Kenneth D Birnbaum
- Center for Genomics and Systems Biology New York University 12 Waverly Place, New York NY 10003 USA
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR 8197 Institut National de la Santé et de la Recherche Médicale (INSERM) U1024 Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05 France; Laboratoire de Reproduction et Développement des Plantes, Centre National de la Recherche Scientifique (CNRS) UMR 5667, Institut National de la Recherche Agronomique (INRA) UMR 879, Ecole Normale Supérieure de LyonUniversité Lyon 1 (UCBL) 46 Allée d'Italie, 69364 Lyon Cedex 07 France
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106
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Ramachandran S, Ahmad K, Henikoff S. Capitalizing on disaster: Establishing chromatin specificity behind the replication fork. Bioessays 2017; 39. [PMID: 28133760 PMCID: PMC5513704 DOI: 10.1002/bies.201600150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic genomes are packaged into nucleosomal chromatin, and genomic activity requires the precise localization of transcription factors, histone modifications and nucleosomes. Classic work described the progressive reassembly and maturation of bulk chromatin behind replication forks. More recent proteomics has detailed the molecular machines that accompany the replicative polymerase to promote rapid histone deposition onto the newly replicated DNA. However, localized chromatin features are transiently obliterated by DNA replication every S phase of the cell cycle. Genomic strategies now observe the rebuilding of locus-specific chromatin features, and reveal surprising delays in transcription factor binding behind replication forks. This implies that transient chromatin disorganization during replication is a central juncture for targeted transcription factor binding within genomes. We propose that transient occlusion of regulatory elements by disorganized nucleosomes during chromatin maturation enforces specificity of factor binding.
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Affiliation(s)
- Srinivas Ramachandran
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
| | - Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
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107
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Reiter F, Wienerroither S, Stark A. Combinatorial function of transcription factors and cofactors. Curr Opin Genet Dev 2017; 43:73-81. [PMID: 28110180 DOI: 10.1016/j.gde.2016.12.007] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/14/2016] [Accepted: 12/21/2016] [Indexed: 12/31/2022]
Abstract
Differential gene expression gives rise to the many cell types of complex organisms. Enhancers regulate transcription by binding transcription factors (TFs), which in turn recruit cofactors to activate RNA Polymerase II at core promoters. Transcriptional regulation is typically mediated by distinct combinations of TFs, enabling a relatively small number of TFs to generate a large diversity of cell types. However, how TFs achieve combinatorial enhancer control and how enhancers, enhancer-bound TFs, and the cofactors they recruit regulate RNA Polymerase II activity is not entirely clear. Here, we review how TF synergy is mediated at the level of DNA binding and after binding, the role of cofactors and the post-translational modifications they catalyze, and discuss different models of enhancer-core-promoter communication.
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Affiliation(s)
- Franziska Reiter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Sebastian Wienerroither
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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108
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Pálfy M, Joseph SR, Vastenhouw NL. The timing of zygotic genome activation. Curr Opin Genet Dev 2017; 43:53-60. [PMID: 28088031 DOI: 10.1016/j.gde.2016.12.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 12/20/2022]
Abstract
After fertilization, the embryonic genome is inactive until transcription is initiated during the maternal-to-zygotic transition. How the onset of transcription is regulated in a precisely timed manner, however, is a long standing question in biology. Several mechanisms have been shown to contribute to the temporal regulation of genome activation but none of them can fully explain the general absence of transcription as well the gene specific onset that follows. Here we review the work that has been done toward elucidating the mechanisms underlying the temporal regulation of transcription in embryos.
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Affiliation(s)
- Máté Pálfy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Shai R Joseph
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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109
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Alabert C, Jasencakova Z, Groth A. Chromatin Replication and Histone Dynamics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:311-333. [PMID: 29357065 DOI: 10.1007/978-981-10-6955-0_15] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Inheritance of the DNA sequence and its proper organization into chromatin is fundamental for genome stability and function. Therefore, how specific chromatin structures are restored on newly synthesized DNA and transmitted through cell division remains a central question to understand cell fate choices and self-renewal. Propagation of genetic information and chromatin-based information in cycling cells entails genome-wide disruption and restoration of chromatin, coupled with faithful replication of DNA. In this chapter, we describe how cells duplicate the genome while maintaining its proper organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure to reassemble nucleosomes at replication forks blocks DNA replication progression in higher eukaryotes and leads to genomic instability, we further underline the importance of the mechanistic link between DNA replication and chromatin duplication.
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Affiliation(s)
- Constance Alabert
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zuzana Jasencakova
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Health and Medical Faculty, University of Copenhagen, Copenhagen, Denmark.
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110
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Festuccia N, Gonzalez I, Navarro P. The Epigenetic Paradox of Pluripotent ES Cells. J Mol Biol 2016; 429:1476-1503. [PMID: 27988225 DOI: 10.1016/j.jmb.2016.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 12/15/2022]
Abstract
The propagation and maintenance of gene expression programs are at the foundation of the preservation of cell identity. A large and complex set of epigenetic mechanisms enables the long-term stability and inheritance of transcription states. A key property of authentic epigenetic regulation is being independent from the instructive signals used for its establishment. This makes epigenetic regulation, particularly epigenetic silencing, extremely robust and powerful to lock regulatory states and stabilise cell identity. In line with this, the establishment of epigenetic silencing during development restricts cell potency and maintains the cell fate choices made by transcription factors (TFs). However, how more immature cells that have not yet established their definitive fate maintain their transitory identity without compromising their responsiveness to signalling cues remains unclear. A paradigmatic example is provided by pluripotent embryonic stem (ES) cells derived from a transient population of cells of the blastocyst. Here, we argue that ES cells represent an interesting "epigenetic paradox": even though they are captured in a self-renewing state characterised by extremely efficient maintenance of their identity, which is a typical manifestation of robust epigenetic regulation, they seem not to heavily rely on classical epigenetic mechanisms. Indeed, self-renewal strictly depends on the TFs that previously instructed their undifferentiated identity and relies on a particular signalling-dependent chromatin state where repressive chromatin marks play minor roles. Although this "epigenetic paradox" may underlie their exquisite responsiveness to developmental cues, it suggests that alternative mechanisms to faithfully propagate gene regulatory states might be prevalent in ES cells.
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Affiliation(s)
- Nicola Festuccia
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Inma Gonzalez
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France
| | - Pablo Navarro
- Epigenetics of Stem Cells, Department of Stem Cell and Developmental Biology, Institut Pasteur, CNRS UMR3738, 25 rue du Docteur Roux, 75015 Paris, France.
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111
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Morao AK, Bouyer D, Roudier F. Emerging concepts in chromatin-level regulation of plant cell differentiation: timing, counting, sensing and maintaining. CURRENT OPINION IN PLANT BIOLOGY 2016; 34:27-34. [PMID: 27522467 DOI: 10.1016/j.pbi.2016.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 07/26/2016] [Accepted: 07/30/2016] [Indexed: 05/04/2023]
Abstract
Plants are characterized by a remarkable phenotypic plasticity that meets the constraints of a sessile lifestyle and the need to adjust constantly to the environment. Recent studies have begun to reveal how chromatin dynamics participate in coordinating cell proliferation and differentiation in response to developmental cues as well as environmental fluctuations. In this review, we discuss the pivotal function of chromatin-based mechanisms in cell fate acquisition and maintenance, within as well as outside meristems. In particular, we highlight the emerging role of specific epigenomic factors and chromatin pathways in timing the activity of stem cells, counting cell divisions and positioning cell fate transitions by sensing phytohormone gradients.
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Affiliation(s)
- Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France
| | - Daniel Bouyer
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France.
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France; Laboratoire de Reproduction et Développement des Plantes, Centre National de la Recherche Scientifique (CNRS) UMR5667, Institut National de la Recherche Agronomique (INRA) UMR879, Ecole Normale Supérieure de Lyon, Université Lyon 1 (UCBL), 46 Allée d'Italie, 69364 Lyon Cedex 07, France.
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112
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Blythe SA, Wieschaus EF. Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis. eLife 2016; 5:20148. [PMID: 27879204 PMCID: PMC5156528 DOI: 10.7554/elife.20148] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/21/2016] [Indexed: 12/18/2022] Open
Abstract
During embryogenesis, the initial chromatin state is established during a period of rapid proliferative activity. We have measured with 3-min time resolution how heritable patterns of chromatin structure are initially established and maintained during the midblastula transition (MBT). We find that regions of accessibility are established sequentially, where enhancers are opened in advance of promoters and insulators. These open states are stably maintained in highly condensed mitotic chromatin to ensure faithful inheritance of prior accessibility status across cell divisions. The temporal progression of establishment is controlled by the biological timers that control the onset of the MBT. In general, acquisition of promoter accessibility is controlled by the biological timer that measures the nucleo-cytoplasmic (N:C) ratio, whereas timing of enhancer accessibility is regulated independently of the N:C ratio. These different timing classes each associate with binding sites for two transcription factors, GAGA-factor and Zelda, previously implicated in controlling chromatin accessibility at ZGA. DOI:http://dx.doi.org/10.7554/eLife.20148.001
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Affiliation(s)
- Shelby A Blythe
- Howard Hughes Medical Institute, Princeton University, Princeton, United States
| | - Eric F Wieschaus
- Howard Hughes Medical Institute, Princeton University, Princeton, United States
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113
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Bowman GD, McKnight JN. Sequence-specific targeting of chromatin remodelers organizes precisely positioned nucleosomes throughout the genome. Bioessays 2016; 39:1-8. [PMID: 27862071 DOI: 10.1002/bies.201600183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Eukaryotic genomes are functionally organized into chromatin, a compact packaging of nucleoproteins with the basic repeating unit known as the nucleosome. A major focus for the chromatin field has been understanding what rules govern nucleosome positioning throughout the genome, and here we review recent findings using a novel, sequence-targeted remodeling enzyme. Nucleosomes are often packed into evenly spaced arrays that are reproducibly positioned, but how such organization is established and maintained through dramatic events such as DNA replication is poorly understood. We hypothesize that a major fraction of positioned nucleosomes arises from sequence-specific targeting of chromatin remodelers to generate "founding" nucleosomes, providing reproducible, predictable, and condition-specific nucleation sites against which neighboring nucleosomes are packed into evenly spaced arrays.
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Affiliation(s)
- Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
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114
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Brennan LD, Forties RA, Patel SS, Wang MD. DNA looping mediates nucleosome transfer. Nat Commun 2016; 7:13337. [PMID: 27808093 PMCID: PMC5097161 DOI: 10.1038/ncomms13337] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 09/23/2016] [Indexed: 01/18/2023] Open
Abstract
Proper cell function requires preservation of the spatial organization of chromatin modifications. Maintenance of this epigenetic landscape necessitates the transfer of parental nucleosomes to newly replicated DNA, a process that is stringently regulated and intrinsically linked to replication fork dynamics. This creates a formidable setting from which to isolate the central mechanism of transfer. Here we utilized a minimal experimental system to track the fate of a single nucleosome following its displacement, and examined whether DNA mechanics itself, in the absence of any chaperones or assembly factors, may serve as a platform for the transfer process. We found that the nucleosome is passively transferred to available dsDNA as predicted by a simple physical model of DNA loop formation. These results demonstrate a fundamental role for DNA mechanics in mediating nucleosome transfer and preserving epigenetic integrity during replication.
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Affiliation(s)
- Lucy D Brennan
- Department of Physics-Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA
| | - Robert A Forties
- Department of Physics-Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
| | - Michelle D Wang
- Department of Physics-Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York 14853, USA.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14853, USA
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115
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Vasseur P, Tonazzini S, Ziane R, Camasses A, Rando OJ, Radman-Livaja M. Dynamics of Nucleosome Positioning Maturation following Genomic Replication. Cell Rep 2016; 16:2651-2665. [PMID: 27568571 PMCID: PMC5014762 DOI: 10.1016/j.celrep.2016.07.083] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/22/2016] [Accepted: 07/28/2016] [Indexed: 12/31/2022] Open
Abstract
Chromatin is thought to carry epigenetic information from one generation to the next, although it is unclear how such information survives the disruptions of nucleosomal architecture occurring during genomic replication. Here, we measure a key aspect of chromatin structure dynamics during replication—how rapidly nucleosome positions are established on the newly replicated daughter genomes. By isolating newly synthesized DNA marked with 5-ethynyl-2′-deoxyuridine (EdU), we characterize nucleosome positions on both daughter genomes of S. cerevisiae during chromatin maturation. We find that nucleosomes rapidly adopt their mid-log positions at highly transcribed genes, which is consistent with a role for transcription in positioning nucleosomes in vivo. Additionally, experiments in hir1Δ mutants reveal a role for HIR in nucleosome spacing. We also characterized nucleosome positions on the leading and lagging strands, uncovering differences in chromatin maturation dynamics at hundreds of genes. Our data define the maturation dynamics of newly replicated chromatin and support a role for transcription in sculpting the chromatin template. Nucleosome positions are determined on newly replicated DNA Transcription reorders nucleosomes in gene bodies after DNA replication The HIR complex tightens nucleosome spacing in gene bodies following replication Nucleosome positions on leading and lagging strands depend on genes’ orientation
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Affiliation(s)
- Pauline Vasseur
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Saphia Tonazzini
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Rahima Ziane
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Alain Camasses
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Marta Radman-Livaja
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France.
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116
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Obier N, Bonifer C. Chromatin programming by developmentally regulated transcription factors: lessons from the study of haematopoietic stem cell specification and differentiation. FEBS Lett 2016; 590:4105-4115. [PMID: 27497427 DOI: 10.1002/1873-3468.12343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/26/2016] [Accepted: 07/31/2016] [Indexed: 01/08/2023]
Abstract
Although the body plan of individuals is encoded in their genomes, each cell type expresses a different gene expression programme and therefore has access to only a subset of this information. Alterations to gene expression programmes are the underlying basis for the differentiation of multiple cell types and are driven by tissue-specific transcription factors (TFs) that interact with the epigenetic regulatory machinery to programme the chromatin landscape into transcriptionally active and inactive states. The haematopoietic system has long served as a paradigm for studying the molecular principles that regulate gene expression in development. In this review article, we summarize the current knowledge on the mechanism of action of TFs regulating haematopoietic stem cell specification and differentiation, and place this information into the context of general principles governing development.
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Affiliation(s)
- Nadine Obier
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
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117
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Sun L, Zhang Y, Zhang Z, Zheng Y, Du L, Zhu B. Preferential Protection of Genetic Fidelity within Open Chromatin by the Mismatch Repair Machinery. J Biol Chem 2016; 291:17692-705. [PMID: 27382058 DOI: 10.1074/jbc.m116.719971] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 12/30/2022] Open
Abstract
Epigenetic systems are well known for the roles they play in regulating the differential expression of the same genome in different cell types. However, epigenetic systems can also directly impact genomic integrity by protecting genetic sequences. Using an experimental evolutionary approach, we studied rates of mutation in the fission yeast Schizosaccharomyces pombe strains that lacked genes encoding several epigenetic regulators or mismatch repair components. We report that loss of a functional mismatch repair pathway in S. pombe resulted in the preferential enrichment of mutations in euchromatin, indicating that the mismatch repair machinery preferentially protected genetic fidelity in euchromatin. This preference is probably determined by differences in the accessibility of chromatin at distinct chromatin regions, which is supported by our observations that chromatin accessibility positively correlated with mutation rates in S. pombe or human cancer samples with deficiencies in mismatch repair. Importantly, such positive correlation was not observed in S. pombe strains or human cancer samples with functional mismatch repair machinery.
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Affiliation(s)
- Lue Sun
- From the Tsinghua University-Peking University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, the National Institute of Biological Sciences, Beijing 102206, and
| | - Yan Zhang
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101
| | - Zhuqiang Zhang
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101
| | - Yong Zheng
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101
| | - Lilin Du
- the National Institute of Biological Sciences, Beijing 102206, and
| | - Bing Zhu
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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