51
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Kinetics and mechanisms of mitotic inheritance of DNA methylation and their roles in aging-associated methylome deterioration. Cell Res 2020; 30:980-996. [PMID: 32581343 DOI: 10.1038/s41422-020-0359-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
Mitotic inheritance of the DNA methylome is a challenging task for the maintenance of cell identity. Whether DNA methylation pattern in different genomic contexts can all be faithfully maintained is an open question. A replication-coupled DNA methylation maintenance model was proposed decades ago, but some observations suggest that a replication-uncoupled maintenance mechanism exists. However, the capacity and the underlying molecular events of replication-uncoupled maintenance are unclear. By measuring maintenance kinetics at the single-molecule level and assessing mutant cells with perturbation of various mechanisms, we found that the kinetics of replication-coupled maintenance are governed by the UHRF1-Ligase 1 and PCNA-DNMT1 interactions, whereas nucleosome occupancy and the interaction between UHRF1 and methylated H3K9 specifically regulate replication-uncoupled maintenance. Surprisingly, replication-uncoupled maintenance is sufficiently robust to largely restore the methylome when replication-coupled maintenance is severely impaired. However, solo-WCGW sites and other CpG sites displaying aging- and cancer-associated hypomethylation exhibit low maintenance efficiency, suggesting that although quite robust, mitotic inheritance of methylation is imperfect and that this imperfection may contribute to selective hypomethylation during aging and tumorigenesis.
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52
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Wang X, Cairns MJ, Yan J. Super-enhancers in transcriptional regulation and genome organization. Nucleic Acids Res 2020; 47:11481-11496. [PMID: 31724731 PMCID: PMC7145697 DOI: 10.1093/nar/gkz1038] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/19/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
Gene expression is precisely controlled in a stage and cell-type-specific manner, largely through the interaction between cis-regulatory elements and their associated trans-acting factors. Where these components aggregate in promoters and enhancers, they are able to cooperate to modulate chromatin structure and support the engagement in long-range 3D superstructures that shape the dynamics of a cell's genomic architecture. Recently, the term 'super-enhancer' has been introduced to describe a hyper-active regulatory domain comprising a complex array of sequence elements that work together to control the key gene networks involved in cell identity. Here, we survey the unique characteristics of super-enhancers compared to other enhancer types and summarize the recent advances in our understanding of their biological role in gene regulation. In particular, we discuss their capacity to attract the formation of phase-separated condensates, and capacity to generate three-dimensional genome structures that precisely activate their target genes. We also propose a multi-stage transition model to explain the evolutionary pressure driving the development of super-enhancers in complex organisms, and highlight the potential for involvement in tumorigenesis. Finally, we discuss more broadly the role of super-enhancers in human health disorders and related potential in therapeutic interventions.
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Affiliation(s)
- Xi Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education / School of Life Sciences, Northwest University, Xi'an 710069, China.,Division of Theoretical Systems Biology, Germany Cancer Research Center, Heidelberg 69115, Germany.,School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.,Centre for Brain and Mental Health Research, University of Newcastle, Callaghan, NSW 2308, Australia; and Hunter Medical Research Institute
| | - Jian Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education / School of Life Sciences, Northwest University, Xi'an 710069, China.,Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong S.A.R., China
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53
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Wheeler E, Brooks AM, Concia L, Vera DL, Wear EE, LeBlanc C, Ramu U, Vaughn MW, Bass HW, Martienssen RA, Thompson WF, Hanley-Bowdoin L. Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin. PLANT PHYSIOLOGY 2020; 183:206-220. [PMID: 32205451 PMCID: PMC7210620 DOI: 10.1104/pp.19.01520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/03/2020] [Indexed: 05/04/2023]
Abstract
The selection and firing of DNA replication origins play key roles in ensuring that eukaryotes accurately replicate their genomes. This process is not well documented in plants due in large measure to difficulties in working with plant systems. We developed a new functional assay to label and map very early replicating loci that must, by definition, include at least a subset of replication origins. Arabidopsis (Arabidopsis thaliana) cells were briefly labeled with 5-ethynyl-2'-deoxy-uridine, and nuclei were subjected to two-parameter flow sorting. We identified more than 5500 loci as initiation regions (IRs), the first regions to replicate in very early S phase. These were classified as strong or weak IRs based on the strength of their replication signals. Strong initiation regions were evenly spaced along chromosomal arms and depleted in centromeres, while weak initiation regions were enriched in centromeric regions. IRs are AT-rich sequences flanked by more GC-rich regions and located predominantly in intergenic regions. Nuclease sensitivity assays indicated that IRs are associated with accessible chromatin. Based on these observations, initiation of plant DNA replication shows some similarity to, but is also distinct from, initiation in other well-studied eukaryotic systems.
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Affiliation(s)
- Emily Wheeler
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Ashley M Brooks
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Lorenzo Concia
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Daniel L Vera
- Florida State University, Center for Genomics and Personalized Medicine, Tallahassee, Florida 32306
| | - Emily E Wear
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Umamaheswari Ramu
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas 78758
| | - Hank W Bass
- Florida State University, Department of Biological Science, Tallahassee, Florida 32306
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - William F Thompson
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
| | - Linda Hanley-Bowdoin
- North Carolina State University, Department of Plant and Microbial Biology, Raleigh, North Carolina 27695
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54
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Ramani V, Qiu R, Shendure J. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Rep 2020; 26:2465-2476.e4. [PMID: 30811994 PMCID: PMC6582983 DOI: 10.1016/j.celrep.2019.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/07/2018] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
A complete view of eukaryotic gene regulation requires that we accurately delineate how transcription factors (TFs) and nucleosomes are arranged along linear DNA in a sensitive, unbiased manner. Here we introduce MNase-SSP, a single-stranded sequencing library preparation method for nuclease-digested chromatin that enables simultaneous mapping of TF and nucleosome positions. As a proof of concept, we apply MNase-SSP toward the genome-wide, high-resolution mapping of nucleosome and TF occupancy in murine embryonic stem cells (mESCs). Compared with existing MNase-seq protocols, MNase-SSP markedly enriches for short DNA fragments, enabling detection of binding by subnucleosomal particles and TFs, in addition to nucleosomes. From these same data, we identify multiple, sequence-dependent binding modes of the architectural TF Ctcf and extend this analysis to the TF Nrsf/ Rest. Looking forward, we anticipate that single stranded protocol (SSP) adaptations of any protein-DNA interaction mapping technique (e.g., ChIP-exo and CUT&RUN) will enhance the information content of the resulting data. Ramani et al. describe MNase-SSP, a single-stranded DNA sequencing library preparation method for profiling chromatin structure. MNase-SSP libraries harbor diminished sequence bias and capture shorter DNA fragments compared to traditional MNase-seq libraries. Applying MNase-SSP to murine embryonic stem cells enables simultaneous analysis of nucleosomal, subnucleosomal, and transcription factor-DNA interactions genome-wide.
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Affiliation(s)
- Vijay Ramani
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA.
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55
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Stewart-Morgan KR, Petryk N, Groth A. Chromatin replication and epigenetic cell memory. Nat Cell Biol 2020; 22:361-371. [PMID: 32231312 DOI: 10.1038/s41556-020-0487-y] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Propagation of the chromatin landscape across cell divisions is central to epigenetic cell memory. Mechanistic analysis of the interplay between DNA replication, the cell cycle, and the epigenome has provided insights into replication-coupled chromatin assembly and post-replicative chromatin maintenance. These breakthroughs are critical for defining how proliferation impacts the epigenome during cell identity changes in development and disease. Here we review these findings in the broader context of epigenetic inheritance across mitotic cell division.
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Affiliation(s)
- Kathleen R Stewart-Morgan
- The Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Nataliya Petryk
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.,Epigenetics and Cell Fate, UMR7216 CNRS, University of Paris, Paris, France
| | - Anja Groth
- The Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
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56
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Beads on a string-nucleosome array arrangements and folding of the chromatin fiber. Nat Struct Mol Biol 2020; 27:109-118. [PMID: 32042149 DOI: 10.1038/s41594-019-0368-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022]
Abstract
Understanding how the genome is structurally organized as chromatin is essential for understanding its function. Here, we review recent developments that allowed the readdressing of old questions regarding the primary level of chromatin structure, the arrangement of nucleosomes along the DNA and the folding of the nucleosome fiber in nuclear space. In contrast to earlier views of nucleosome arrays as uniformly regular and folded, recent findings reveal heterogeneous array organization and diverse modes of folding. Local structure variations reflect a continuum of functional states characterized by differences in post-translational histone modifications, associated chromatin-interacting proteins and nucleosome-remodeling enzymes.
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57
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Delamarre A, Barthe A, de la Roche Saint-André C, Luciano P, Forey R, Padioleau I, Skrzypczak M, Ginalski K, Géli V, Pasero P, Lengronne A. MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading. Mol Cell 2020; 77:395-410.e3. [PMID: 31759824 DOI: 10.1016/j.molcel.2019.10.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/09/2019] [Accepted: 10/17/2019] [Indexed: 01/04/2023]
Abstract
The recovery of stalled replication forks depends on the controlled resection of nascent DNA and on the loading of cohesin. These processes operate in the context of nascent chromatin, but the impact of nucleosome structure on a fork restart remains poorly understood. Here, we show that the Mre11-Rad50-Xrs2 (MRX) complex acts together with the chromatin modifiers Gcn5 and Set1 and the histone remodelers RSC, Chd1, and Isw1 to promote chromatin remodeling at stalled forks. Increased chromatin accessibility facilitates the resection of nascent DNA by the Exo1 nuclease and the Sgs1 and Chl1 DNA helicases. Importantly, increased ssDNA promotes the recruitment of cohesin to arrested forks in a Scc2-Scc4-dependent manner. Altogether, these results indicate that MRX cooperates with chromatin modifiers to orchestrate the action of remodelers, nucleases, and DNA helicases, promoting the resection of nascent DNA and the loading of cohesin, two key processes involved in the recovery of arrested forks.
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Affiliation(s)
- Axel Delamarre
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Christophe de la Roche Saint-André
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Pierre Luciano
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Ismaël Padioleau
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
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58
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Epigenome Regulation by Dynamic Nucleosome Unwrapping. Trends Biochem Sci 2020; 45:13-26. [PMID: 31630896 PMCID: PMC10168609 DOI: 10.1016/j.tibs.2019.09.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Gene regulation in eukaryotes requires the controlled access of sequence-specific transcription factors (TFs) to their sites in a chromatin landscape dominated by nucleosomes. Nucleosomes are refractory to TF binding, and often must be removed from regulatory regions. Recent genomic studies together with in vitro measurements suggest that the nucleosome barrier to TF binding is modulated by dynamic nucleosome unwrapping governed by ATP-dependent chromatin remodelers. Genome-wide occupancy and the regulation of subnucleosomal intermediates have gained recent attention with the application of high-resolution approaches for precision mapping of protein-DNA interactions. We summarize here recent findings on nucleosome substructures and TF binding dynamics, and highlight how unwrapped nucleosomal intermediates provide a novel signature of active chromatin.
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59
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Oberbeckmann E, Wolff M, Krietenstein N, Heron M, Ellins JL, Schmid A, Krebs S, Blum H, Gerland U, Korber P. Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome. Genome Res 2019; 29:1996-2009. [PMID: 31694866 PMCID: PMC6886505 DOI: 10.1101/gr.253419.119] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022]
Abstract
Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation because nucleosomes modulate DNA access by their positioning along the genome. A cell-population nucleosome map requires two observables: nucleosome positions along the DNA ("Where?") and nucleosome occupancies across the population ("In how many cells?"). All available genome-wide nucleosome mapping techniques are yield methods because they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or nonnucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions, but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby cross-validating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae genome via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9-bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (±SD). Depending on nucleosome position calling procedures, there are 57,000 to 60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but correlate with increased presence of the nucleosome-evicting chromatin structure remodeling (RSC) complex, and are enriched upstream of highly transcribed or regulated genes. Our work provides a quantitative method and reference frame in absolute terms for future chromatin studies.
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Affiliation(s)
- Elisa Oberbeckmann
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Michael Wolff
- Physik Department, Technische Universität München, 85748 Garching, Germany
| | - Nils Krietenstein
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Mark Heron
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jessica L Ellins
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Andrea Schmid
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Stefan Krebs
- Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Ulrich Gerland
- Physik Department, Technische Universität München, 85748 Garching, Germany
| | - Philipp Korber
- Molecular Biology Division, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
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60
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Owens N, Papadopoulou T, Festuccia N, Tachtsidi A, Gonzalez I, Dubois A, Vandormael-Pournin S, Nora EP, Bruneau BG, Cohen-Tannoudji M, Navarro P. CTCF confers local nucleosome resiliency after DNA replication and during mitosis. eLife 2019; 8:e47898. [PMID: 31599722 PMCID: PMC6844645 DOI: 10.7554/elife.47898] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The access of Transcription Factors (TFs) to their cognate DNA binding motifs requires a precise control over nucleosome positioning. This is especially important following DNA replication and during mitosis, both resulting in profound changes in nucleosome organization over TF binding regions. Using mouse Embryonic Stem (ES) cells, we show that the TF CTCF displaces nucleosomes from its binding site and locally organizes large and phased nucleosomal arrays, not only in interphase steady-state but also immediately after replication and during mitosis. Correlative analyses suggest this is associated with fast gene reactivation following replication and mitosis. While regions bound by other TFs (Oct4/Sox2), display major rearrangement, the post-replication and mitotic nucleosome positioning activity of CTCF is not unique: Esrrb binding regions are also characterized by persistent nucleosome positioning. Therefore, selected TFs such as CTCF and Esrrb act as resilient TFs governing the inheritance of nucleosome positioning at regulatory regions throughout the cell-cycle.
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Affiliation(s)
- Nick Owens
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Thaleia Papadopoulou
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Nicola Festuccia
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Alexandra Tachtsidi
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
- Sorbonne Université, Collège DoctoralParisFrance
| | - Inma Gonzalez
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Agnes Dubois
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
| | - Sandrine Vandormael-Pournin
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR 3738ParisFrance
| | - Elphège P Nora
- Gladstone InstitutesSan FranciscoUnited States
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
| | - Benoit G Bruneau
- Gladstone InstitutesSan FranciscoUnited States
- Cardiovascular Research InstituteUniversity of California, San FranciscoSan FranciscoUnited States
- Department of PediatricsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Michel Cohen-Tannoudji
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Early Mammalian Development and Stem Cell Biology, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR 3738ParisFrance
| | - Pablo Navarro
- Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell BiologyInstitut Pasteur, CNRS UMR3738ParisFrance
- Equipe Labellisée LIGUE Contre le CancerParisFrance
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61
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Affiliation(s)
- Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109;
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
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62
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Yee WB, Delaney PM, Vanderzalm PJ, Ramachandran S, Fehon RG. The CAF-1 complex couples Hippo pathway target gene expression and DNA replication. Mol Biol Cell 2019; 30:2929-2942. [PMID: 31553691 PMCID: PMC6822585 DOI: 10.1091/mbc.e19-07-0387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Hippo signaling pathway regulates tissue growth and organ development in many animals, including humans. Pathway activity leads to inactivation of Yorkie (Yki), a transcriptional coactivator that drives expression of growth-promoting genes. In addition, Yki has been shown to recruit chromatin modifiers that enhance chromatin accessibility and thereby enhance Yki function. Here, we asked whether changes in chromatin accessibility that occur during DNA replication could also affect Yki function. We found that depletion of the chromatin assembly complex-1 (CAF-1) complex, a histone chaperone that is required for nucleosome assembly after DNA replication, in the wing imaginal epithelium leads to increased Hippo pathway target gene expression but does not affect expression of other genes. Yki shows greater association with target sites when CAF-1 is depleted and misregulation of target gene expression is Yki-dependent, suggesting that nucleosome assembly competes with Yki for pathway targets post-DNA replication. Consistent with this idea, increased target gene expression is DNA replication dependent and newly replicated chromatin at target sites shows marked nucleosome depletion when CAF-1 function is reduced. These observations suggest a connection between cell cycle progression and Hippo pathway target expression, providing insights into functions of the Hippo pathway in normal and abnormal tissue growth.
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Affiliation(s)
- William B Yee
- Department of Molecular Genetics and Cell Biology.,Graduate Program in Cell and Molecular Biology, and
| | | | - Pamela J Vanderzalm
- Department of Molecular Genetics and Cell Biology.,Department of Biology, John Carroll University, University Heights, OH 44118
| | - Srinivas Ramachandran
- RNA Bioscience Initiative and.,Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Richard G Fehon
- Department of Molecular Genetics and Cell Biology.,Graduate Program in Cell and Molecular Biology, and
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63
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Meers MP, Janssens DH, Henikoff S. Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded. Mol Cell 2019; 75:562-575.e5. [PMID: 31253573 PMCID: PMC6697550 DOI: 10.1016/j.molcel.2019.05.025] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/30/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022]
Abstract
Although the in vitro structural and in vivo spatial characteristics of transcription factor (TF) binding are well defined, TF interactions with chromatin and other companion TFs during development are poorly understood. To analyze such interactions in vivo, we profiled several TFs across a time course of human embryonic stem cell differentiation and studied their interactions with nucleosomes and co-occurring TFs by enhanced chromatin occupancy (EChO), a computational strategy for classifying TF interactions with chromatin. EChO shows that multiple individual TFs can employ either direct DNA binding or "pioneer" nucleosome binding at different enhancer targets. Nucleosome binding is not exclusively confined to inaccessible chromatin but rather correlated with local binding of other TFs and degeneracy at key bases in the pioneer factor target motif responsible for direct DNA binding. Our strategy reveals a dynamic exchange of TFs at enhancers across developmental time that is aided by pioneer nucleosome binding.
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Affiliation(s)
- Michael P Meers
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA
| | - Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA; Howard Hughes Medical Institute, USA.
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64
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Talbert PB, Meers MP, Henikoff S. Old cogs, new tricks: the evolution of gene expression in a chromatin context. Nat Rev Genet 2019; 20:283-297. [PMID: 30886348 DOI: 10.1038/s41576-019-0105-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sophisticated gene-regulatory mechanisms probably evolved in prokaryotes billions of years before the emergence of modern eukaryotes, which inherited the same basic enzymatic machineries. However, the epigenomic landscapes of eukaryotes are dominated by nucleosomes, which have acquired roles in genome packaging, mitotic condensation and silencing parasitic genomic elements. Although the molecular mechanisms by which nucleosomes are displaced and modified have been described, just how transcription factors, histone variants and modifications and chromatin regulators act on nucleosomes to regulate transcription is the subject of considerable ongoing study. We explore the extent to which these transcriptional regulatory components function in the context of the evolutionarily ancient role of chromatin as a barrier to processes acting on DNA and how chromatin proteins have diversified to carry out evolutionarily recent functions that accompanied the emergence of differentiation and development in multicellular eukaryotes.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael P Meers
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
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65
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Abstract
Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. In this Review, we examine how the accessible genome is measured and explore the role of transcription factors in initiating accessibility remodelling; our goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.
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Affiliation(s)
- Sandy L Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg BioHub, San Francisco, CA, USA.
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66
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Faria J, Glover L, Hutchinson S, Boehm C, Field MC, Horn D. Monoallelic expression and epigenetic inheritance sustained by a Trypanosoma brucei variant surface glycoprotein exclusion complex. Nat Commun 2019; 10:3023. [PMID: 31289266 PMCID: PMC6617441 DOI: 10.1038/s41467-019-10823-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 06/04/2019] [Indexed: 02/06/2023] Open
Abstract
The largest gene families in eukaryotes are subject to allelic exclusion, but mechanisms underpinning single allele selection and inheritance remain unclear. Here, we describe a protein complex sustaining variant surface glycoprotein (VSG) allelic exclusion and antigenic variation in Trypanosoma brucei parasites. The VSG-exclusion-1 (VEX1) protein binds both telomeric VSG-associated chromatin and VEX2, an ortholog of nonsense-mediated-decay helicase, UPF1. VEX1 and VEX2 assemble in an RNA polymerase-I transcription-dependent manner and sustain the active, subtelomeric VSG-associated transcription compartment. VSG transcripts and VSG coats become highly heterogeneous when VEX proteins are depleted. Further, the DNA replication-associated chromatin assembly factor, CAF-1, binds to and specifically maintains VEX1 compartmentalisation following DNA replication. Thus, the VEX-complex controls VSG-exclusion, while CAF-1 sustains VEX-complex inheritance in association with the active-VSG. Notably, the VEX2-orthologue and CAF-1 in mammals are also implicated in exclusion and inheritance functions. In trypanosomes, these factors sustain a highly effective and paradigmatic immune evasion strategy.
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Affiliation(s)
- Joana Faria
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Lucy Glover
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
- Trypanosome Molecular Biology, Department of Parasites and Insect Vectors, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015, Paris, France
| | - Sebastian Hutchinson
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
- Trypanosome Cell Biology Unit, INSERM U1201, Department of Parasites and Insect Vectors, Institut Pasteur, 25-28 Rue du Docteur Roux, 75015, Paris, France
| | - Cordula Boehm
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Mark C Field
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - David Horn
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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67
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Li Y, Ai S, Yu X, Li C, Li X, Yue Y, Wei Y, Li CY, He A. Replication-Independent Histone Turnover Underlines the Epigenetic Homeostasis in Adult Heart. Circ Res 2019; 125:198-208. [PMID: 31104571 DOI: 10.1161/circresaha.118.314366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RATIONALE Replication-independent histone turnover has been linked to cis-regulatory chromatin domains in cultured cell lines, but its molecular underpinnings and functional relevance in adult mammalian tissues remain yet to be defined. OBJECTIVE We investigated regulatory functions of replication-independent histone turnover in chromatin states of postmitotic cardiomyocytes from adult mouse heart. METHODS AND RESULTS We used H2B-GFP (histone 2B-green fluorescent protein) fusion protein pulse-and-chase approaches to measure histone turnover rate in mouse cardiomyocytes. Surprisingly, we found that the short histone half-life (≈2 weeks) contrasted dramatically with the long lifetime of cardiomyocytes, and rapid histone turnover regions corresponded to cis-regulatory domains of heart genes. Interestingly, recruitment of chromatin modifiers, including Polycomb EED (embryonic ectoderm development), was positively correlated with histone turnover rate at enhancers. Mechanistically, through directly interacting with and engaging the BAF (BRG1 [Brahma-related gene-1]-associated factor) complex for nucleosome exchange for stereotyped histone modifications from the free histone pool, EED augmented histone turnover to restrain enhancer overactivation. CONCLUSIONS We propose a model in which replication-independent histone turnover reinforces robustness of local chromatin states for adult tissue homeostasis.
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Affiliation(s)
- Yumei Li
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, China (Y.L., S.A., C.L., X.L., Y.Y., C.-Y.L., A.H.)
| | - Shanshan Ai
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, China (Y.L., S.A., C.L., X.L., Y.Y., C.-Y.L., A.H.)
| | - Xianhong Yu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China (X.Y., A.H.)
| | - Chen Li
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, China (Y.L., S.A., C.L., X.L., Y.Y., C.-Y.L., A.H.)
| | - Xin Li
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, China (Y.L., S.A., C.L., X.L., Y.Y., C.-Y.L., A.H.)
| | - Yanzhu Yue
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, China (Y.L., S.A., C.L., X.L., Y.Y., C.-Y.L., A.H.)
| | - Yusheng Wei
- College of Life Science, Peking University, Beijing, China (Y.W.)
| | - Chuan-Yun Li
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, China (Y.L., S.A., C.L., X.L., Y.Y., C.-Y.L., A.H.)
| | - Aibin He
- From the Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, China (Y.L., S.A., C.L., X.L., Y.Y., C.-Y.L., A.H.).,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China (X.Y., A.H.)
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68
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Stewart-Morgan KR, Reverón-Gómez N, Groth A. Transcription Restart Establishes Chromatin Accessibility after DNA Replication. Mol Cell 2019; 75:284-297.e6. [DOI: 10.1016/j.molcel.2019.04.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/29/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022]
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69
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Barel I, Reich NO, Brown FLH. Integrated rate laws for processive and distributive enzymatic turnover. J Chem Phys 2019; 150:244120. [PMID: 31255081 DOI: 10.1063/1.5097576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recently derived steady-state differential rate laws for the catalytic turnover of molecules containing two substrate sites are reformulated as integrated rate laws. The analysis applies to a broad class of Markovian dynamic models, motivated by the varied and often complex mechanisms associated with DNA modifying enzymes. Analysis of experimental data for the methylation kinetics of DNA by Dam (DNA adenine methyltransferase) is drastically improved through the use of integrated rate laws. Data that are too noisy for fitting to differential predictions are reliably interpreted through the integrated rate laws.
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Affiliation(s)
- Itay Barel
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Frank L H Brown
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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70
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Gutiérrez MP, MacAlpine HK, MacAlpine DM. Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork. Genome Res 2019; 29:1123-1133. [PMID: 31217252 PMCID: PMC6633257 DOI: 10.1101/gr.243386.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 05/28/2019] [Indexed: 01/06/2023]
Abstract
Proper regulation and maintenance of the epigenome is necessary to preserve genome function. However, in every cell division, the epigenetic state is disassembled and then reassembled in the wake of the DNA replication fork. Chromatin restoration on nascent DNA is a complex and regulated process that includes nucleosome assembly and remodeling, deposition of histone variants, and the re-establishment of transcription factor binding. To study the genome-wide dynamics of chromatin restoration behind the DNA replication fork, we developed nascent chromatin occupancy profiles (NCOPs) to comprehensively profile nascent and mature chromatin at nucleotide resolution. Although nascent chromatin is inherently less organized than mature chromatin, we identified locus-specific differences in the kinetics of chromatin maturation that were predicted by the epigenetic landscape, including the histone variant H2AZ, which marked loci with rapid maturation kinetics. The chromatin maturation at origins of DNA replication was dependent on whether the origin underwent initiation or was passively replicated from distal-originating replication forks, suggesting distinct chromatin assembly mechanisms surrounding activated and disassembled prereplicative complexes. Finally, we identified sites that were only occupied transiently by DNA-binding factors following passage of the replication fork, which may provide a mechanism for perturbations of the DNA replication program to shape the regulatory landscape of the genome.
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Affiliation(s)
- Mónica P Gutiérrez
- University Program in Genetics and Genomics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David M MacAlpine
- University Program in Genetics and Genomics, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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71
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Rasmussen KD, Berest I, Keβler S, Nishimura K, Simón-Carrasco L, Vassiliou GS, Pedersen MT, Christensen J, Zaugg JB, Helin K. TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Res 2019; 29:564-575. [PMID: 30796038 PMCID: PMC6442383 DOI: 10.1101/gr.239277.118] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 02/19/2019] [Indexed: 12/17/2022]
Abstract
The epigenetic regulator TET2 is frequently mutated in hematological diseases. Mutations have been shown to arise in hematopoietic stem cells early in disease development and lead to altered DNA methylation landscapes and an increased risk of hematopoietic malignancy. Here, we show by genome-wide mapping of TET2 binding sites in different cell types that TET2 localizes to regions of open chromatin and cell-type-specific enhancers. We find that deletion of Tet2 in native hematopoiesis as well as fully transformed acute myeloid leukemia (AML) results in changes in transcription factor (TF) activity within these regions, and we provide evidence that loss of TET2 leads to attenuation of chromatin binding of members of the basic helix-loop-helix (bHLH) TF family. Together, these findings demonstrate that TET2 activity shapes the local chromatin environment at enhancers to facilitate TF binding and provides an example of how epigenetic dysregulation can affect gene expression patterns and drive disease development.
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Affiliation(s)
- Kasper D Rasmussen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ivan Berest
- European Molecular Biology Institute, Structural and Computational Unit, 69115 Heidelberg, Germany
| | - Sandra Keβler
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Koutarou Nishimura
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Lucía Simón-Carrasco
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - George S Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB2 0XY, United Kingdom
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0PT, United Kingdom
| | - Marianne T Pedersen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jesper Christensen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Judith B Zaugg
- European Molecular Biology Institute, Structural and Computational Unit, 69115 Heidelberg, Germany
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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72
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Pherson M, Misulovin Z, Gause M, Dorsett D. Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila. Genome Res 2019; 29:602-612. [PMID: 30796039 PMCID: PMC6442380 DOI: 10.1101/gr.243832.118] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/20/2019] [Indexed: 12/23/2022]
Abstract
Cohesin consists of the SMC1-SMC3-Rad21 tripartite ring and the SA protein that interacts with Rad21. The Nipped-B protein loads cohesin topologically around chromosomes to mediate sister chromatid cohesion and facilitate long-range control of gene transcription. It is largely unknown how Nipped-B and cohesin associate specifically with gene promoters and transcriptional enhancers, or how sister chromatid cohesion is established. Here, we use genome-wide chromatin immunoprecipitation in Drosophila cells to show that SA and the Fs(1)h (BRD4) BET domain protein help recruit Nipped-B and cohesin to enhancers and DNA replication origins, whereas the MED30 subunit of the Mediator complex directs Nipped-B and Vtd in Drosophila (also known as Rad21) to promoters. All enhancers and their neighboring promoters are close to DNA replication origins and bind SA with proportional levels of cohesin subunits. Most promoters are far from origins and lack SA but bind Nipped-B and Rad21 with subproportional amounts of SMC1, indicating that they bind cohesin rings only part of the time. Genetic data show that Nipped-B and Rad21 function together with Fs(1)h to facilitate Drosophila development. These findings show that Nipped-B and cohesin are differentially targeted to enhancers and promoters, and suggest models for how SA and DNA replication help establish sister chromatid cohesion and facilitate enhancer-promoter communication. They indicate that SA is not an obligatory cohesin subunit but a factor that controls cohesin location on chromosomes.
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Affiliation(s)
- Michelle Pherson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, USA
| | - Ziva Misulovin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, USA
| | - Maria Gause
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, USA
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, USA
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73
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Abstract
Two papers in Molecular Cell (Kubik et al., 2018; Yan et al., 2018) explore the mechanisms by which transcription factors bind their sites in chromatin, providing fresh insights into the much-debated question of how transcription factors can be "pioneers."
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Affiliation(s)
- Steven Henikoff
- Fred Hutchinson Cancer Research Center, Basic Sciences Division, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
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74
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McDaniel SL, Gibson TJ, Schulz KN, Fernandez Garcia M, Nevil M, Jain SU, Lewis PW, Zaret KS, Harrison MM. Continued Activity of the Pioneer Factor Zelda Is Required to Drive Zygotic Genome Activation. Mol Cell 2019; 74:185-195.e4. [PMID: 30797686 DOI: 10.1016/j.molcel.2019.01.014] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/10/2018] [Accepted: 01/08/2019] [Indexed: 02/08/2023]
Abstract
Reprogramming cell fate during the first stages of embryogenesis requires that transcriptional activators gain access to the genome and remodel the zygotic transcriptome. Nonetheless, it is not clear whether the continued activity of these pioneering factors is required throughout zygotic genome activation or whether they are only required early to establish cis-regulatory regions. To address this question, we developed an optogenetic strategy to rapidly and reversibly inactivate the master regulator of genome activation in Drosophila, Zelda. Using this strategy, we demonstrate that continued Zelda activity is required throughout genome activation. We show that Zelda binds DNA in the context of nucleosomes and suggest that this allows Zelda to occupy the genome despite the rapid division cycles in the early embryo. These data identify a powerful strategy to inactivate transcription factor function during development and suggest that reprogramming in the embryo may require specific, continuous pioneering functions to activate the genome.
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Affiliation(s)
- Stephen L McDaniel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Katharine N Schulz
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Meilin Fernandez Garcia
- Institute for Regenerative Medicine and Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Markus Nevil
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Siddhant U Jain
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Peter W Lewis
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Epigenetics Program, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison WI 53706, USA.
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75
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Brahma S, Henikoff S. RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast. Mol Cell 2018; 73:238-249.e3. [PMID: 30554944 PMCID: PMC6475595 DOI: 10.1016/j.molcel.2018.10.046] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/04/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023]
Abstract
The classic view of nucleosome organization at active promoters is that two well-positioned nucleosomes flank a nucleosome-depleted region (NDR). However, this view has been recently disputed by contradictory reports as to whether wider (≳150 bp) NDRs instead contain unstable, micrococcal nuclease-sensitive ("fragile") nucleosomal particles. To determine the composition of fragile particles, we introduce CUT&RUN.ChIP, in which targeted nuclease cleavage and release is followed by chromatin immunoprecipitation. We find that fragile particles represent the occupancy of the RSC (remodeling the structure of chromatin) nucleosome remodeling complex and RSC-bound, partially unwrapped nucleosomal intermediates. We also find that general regulatory factors (GRFs) bind to partially unwrapped nucleosomes at these promoters. We propose that RSC binding and its action cause nucleosomes to unravel, facilitate subsequent binding of GRFs, and constitute a dynamic cycle of nucleosome deposition and clearance at the subset of wide Pol II promoter NDRs.
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Affiliation(s)
- Sandipan Brahma
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, USA.
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76
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Abstract
In this issue of Cancer Cell, Volk et al. report that overexpression of CHAF1B displaces myeloid transcription factors from chromatin, and deletion of CHAF1B promotes differentiation of leukemia cells and suppresses leukemogenesis in a murine model, revealing a causal role of and an unexpected mechanism for CHAF1B overexpression in tumorigenesis.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Xu Zhang
- Institute for Cancer Genetics and Department of Pediatrics and Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics and Department of Pediatrics and Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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77
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Thibodeau A, Uyar A, Khetan S, Stitzel ML, Ucar D. A neural network based model effectively predicts enhancers from clinical ATAC-seq samples. Sci Rep 2018; 8:16048. [PMID: 30375457 PMCID: PMC6207744 DOI: 10.1038/s41598-018-34420-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023] Open
Abstract
Enhancers are cis-acting sequences that regulate transcription rates of their target genes in a cell-specific manner and harbor disease-associated sequence variants in cognate cell types. Many complex diseases are associated with enhancer malfunction, necessitating the discovery and study of enhancers from clinical samples. Assay for Transposase Accessible Chromatin (ATAC-seq) technology can interrogate chromatin accessibility from small cell numbers and facilitate studying enhancers in pathologies. However, on average, ~35% of open chromatin regions (OCRs) from ATAC-seq samples map to enhancers. We developed a neural network-based model, Predicting Enhancers from ATAC-Seq data (PEAS), to effectively infer enhancers from clinical ATAC-seq samples by extracting ATAC-seq data features and integrating these with sequence-related features (e.g., GC ratio). PEAS recapitulated ChromHMM-defined enhancers in CD14+ monocytes, CD4+ T cells, GM12878, peripheral blood mononuclear cells, and pancreatic islets. PEAS models trained on these 5 cell types effectively predicted enhancers in four cell types that are not used in model training (EndoC-βH1, naïve CD8+ T, MCF7, and K562 cells). Finally, PEAS inferred individual-specific enhancers from 19 islet ATAC-seq samples and revealed variability in enhancer activity across individuals, including those driven by genetic differences. PEAS is an easy-to-use tool developed to study enhancers in pathologies by taking advantage of the increasing number of clinical epigenomes.
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Affiliation(s)
- Asa Thibodeau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Asli Uyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Shubham Khetan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA. .,Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
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78
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Reverón-Gómez N, González-Aguilera C, Stewart-Morgan KR, Petryk N, Flury V, Graziano S, Johansen JV, Jakobsen JS, Alabert C, Groth A. Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication. Mol Cell 2018; 72:239-249.e5. [PMID: 30146316 PMCID: PMC6202308 DOI: 10.1016/j.molcel.2018.08.010] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/25/2018] [Accepted: 08/07/2018] [Indexed: 12/22/2022]
Abstract
Chromatin organization is disrupted genome-wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naive histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is faithfully copied during DNA replication or the epigenome is perturbed. Here we develop chromatin occupancy after replication (ChOR-seq) to determine histone PTM occupancy immediately after DNA replication and across the cell cycle. We show that H3K4me3, H3K36me3, H3K79me3, and H3K27me3 positional information is reproduced with high accuracy on newly synthesized DNA through histone recycling. Quantitative ChOR-seq reveals that de novo methylation to restore H3K4me3 and H3K27me3 levels occurs across the cell cycle with mark- and locus-specific kinetics. Collectively, this demonstrates that accurate parental histone recycling preserves positional information and allows PTM transmission to daughter cells while modification of new histones gives rise to complex epigenome fluctuations across the cell cycle that could underlie cell-to-cell heterogeneity.
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Affiliation(s)
- Nazaret Reverón-Gómez
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Cristina González-Aguilera
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kathleen R Stewart-Morgan
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nataliya Petryk
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Valentin Flury
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Simona Graziano
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Janus Schou Jakobsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Constance Alabert
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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79
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Deng X, Qiu Q, He K, Cao X. The seekers: how epigenetic modifying enzymes find their hidden genomic targets in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:75-81. [PMID: 29864678 DOI: 10.1016/j.pbi.2018.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/03/2018] [Accepted: 05/12/2018] [Indexed: 05/23/2023]
Abstract
Epigenetic regulation plays fundamental roles in modulating chromatin-based processes and shaping the epigenome in multicellular eukaryotes, including plants. How epigenetic factors recognize their target loci hiding in the vast genomic DNA sequence remains a long-standing mystery. During the past several years, a growing body of work has revealed the complex, dynamic, and diverse chromatin-targeting mechanisms of these epigenetic factors. In this review, we focus on recent advances in understanding the recruitment of epigenetic factors to specific genomic regions, based on data from Arabidopsis thaliana.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Qiu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kaixuan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China.
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80
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81
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The interaction landscape between transcription factors and the nucleosome. Nature 2018; 562:76-81. [PMID: 30250250 PMCID: PMC6173309 DOI: 10.1038/s41586-018-0549-5] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 08/06/2018] [Indexed: 01/01/2023]
Abstract
Nucleosomes cover most of the genome and are thought to be displaced by transcription factors in regions that direct gene expression. However, the modes of interaction between transcription factors and nucleosomal DNA remain largely unknown. Here we systematically explore interactions between the nucleosome and 220 transcription factors representing diverse structural families. Consistent with earlier observations, we find that the majority of the studied transcription factors have less access to nucleosomal DNA than to free DNA. The motifs recovered from transcription factors bound to nucleosomal and free DNA are generally similar. However, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many transcription factors preferentially bind close to the end of nucleosomal DNA, or to periodic positions on the solvent-exposed side of the DNA. In addition, several transcription factors usually bind to nucleosomal DNA in a particular orientation. Some transcription factors specifically interact with DNA located at the dyad position at which only one DNA gyre is wound, whereas other transcription factors prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals notable differences in the binding of transcription factors to free and nucleosomal DNA, and uncovers a diverse interaction landscape between transcription factors and the nucleosome.
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82
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Clément C, Orsi GA, Gatto A, Boyarchuk E, Forest A, Hajj B, Miné-Hattab J, Garnier M, Gurard-Levin ZA, Quivy JP, Almouzni G. High-resolution visualization of H3 variants during replication reveals their controlled recycling. Nat Commun 2018; 9:3181. [PMID: 30093638 PMCID: PMC6085313 DOI: 10.1038/s41467-018-05697-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/05/2018] [Indexed: 12/11/2022] Open
Abstract
DNA replication is a challenge for the faithful transmission of parental information to daughter cells, as both DNA and chromatin organization must be duplicated. Replication stress further complicates the safeguard of epigenome integrity. Here, we investigate the transmission of the histone variants H3.3 and H3.1 during replication. We follow their distribution relative to replication timing, first in the genome and, second, in 3D using super-resolution microscopy. We find that H3.3 and H3.1 mark early- and late-replicating chromatin, respectively. In the nucleus, H3.3 forms domains, which decrease in density throughout replication, while H3.1 domains increase in density. Hydroxyurea impairs local recycling of parental histones at replication sites. Similarly, depleting the histone chaperone ASF1 affects recycling, leading to an impaired histone variant landscape. We discuss how faithful transmission of histone variants involves ASF1 and can be impacted by replication stress, with ensuing consequences for cell fate and tumorigenesis. Epigenetic modifications are a key contributor to cell identity, and their propagation is crucial for proper development. Here the authors use a super-resolution microscopy approach to reveal how histone variants are faithfully transmitted during genome duplication, and reveal an important role for the histone chaperone ASF1 in the redistribution of parental histones.
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Affiliation(s)
- Camille Clément
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Guillermo A Orsi
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Alberto Gatto
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Ekaterina Boyarchuk
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Audrey Forest
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Bassam Hajj
- Institut Curie, PSL Research University, CNRS, UMR168, Laboratoire Physico-Chimie, F-75005, Paris, France
| | - Judith Miné-Hattab
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.,Institut Curie, PSL Research University, CNRS, UMR3664, F-75005, Paris, France
| | - Mickaël Garnier
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.,Institut Curie, PSL Research University, CNRS, UMR3664, F-75005, Paris, France
| | - Zachary A Gurard-Levin
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.,SAMDI Tech, Inc., Chicago, IL, 60657, USA
| | - Jean-Pierre Quivy
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.
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83
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Systematic Study of Nucleosome-Displacing Factors in Budding Yeast. Mol Cell 2018; 71:294-305.e4. [PMID: 30017582 DOI: 10.1016/j.molcel.2018.06.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/04/2018] [Accepted: 06/07/2018] [Indexed: 12/11/2022]
Abstract
Nucleosomes present a barrier for the binding of most transcription factors (TFs). However, special TFs known as nucleosome-displacing factors (NDFs) can access embedded sites and cause the depletion of the local nucleosomes as well as repositioning of the neighboring nucleosomes. Here, we developed a novel high-throughput method in yeast to identify NDFs among 104 TFs and systematically characterized the impact of orientation, affinity, location, and copy number of their binding motifs on the nucleosome occupancy. Using this assay, we identified 29 NDF motifs and divided the nuclear TFs into three groups with strong, weak, and no nucleosome-displacing activities. Further studies revealed that tight DNA binding is the key property that underlies NDF activity, and the NDFs may partially rely on the DNA replication to compete with nucleosome. Overall, our study presents a framework to functionally characterize NDFs and elucidate the mechanism of nucleosome invasion.
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84
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Madamba EV, Berthet EB, Francis NJ. Inheritance of Histones H3 and H4 during DNA Replication In Vitro. Cell Rep 2018; 21:1361-1374. [PMID: 29091772 DOI: 10.1016/j.celrep.2017.10.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/24/2017] [Accepted: 10/06/2017] [Indexed: 01/08/2023] Open
Abstract
Nucleosomes are believed to carry epigenetic information through the cell cycle, including through DNA replication. It has been known for decades that parental histones are reassembled on newly replicated chromatin, but the mechanisms underlying histone inheritance and dispersal during DNA replication are not fully understood. We monitored the fate of histones H3 or H4 from a single nucleosome through DNA replication in two in vitro systems. In the SV40 system, histones assembled on a single nucleosome positioning sequence can be inherited by their own daughter DNA but are dispersed from their original location. In Xenopus laevis extracts, histones are dynamic, and nucleosomes are repositioned independent of and prior to DNA replication. Nevertheless, a high fraction of histones H3 and H4 that are inherited through DNA replication remains near its starting location. Thus, inheritance of histone proteins and their dispersal can be mechanistically uncoupled.
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Affiliation(s)
- Egbert Vincent Madamba
- Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Ellora Bellows Berthet
- Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Nicole Jane Francis
- Institut de recherches clinique de Montréal (IRCM) and Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC H2W 1R7 Canada.
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85
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Bameta T, Das D, Padinhateeri R. Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer. Nucleic Acids Res 2018; 46:4991-5000. [PMID: 29850895 PMCID: PMC6007630 DOI: 10.1093/nar/gky207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/09/2018] [Indexed: 01/09/2023] Open
Abstract
Positioning of nucleosomes along the genomic DNA is crucial for many cellular processes that include gene regulation and higher order packaging of chromatin. The question of how nucleosome-positioning information from a parent chromatin gets transferred to the daughter chromatin is highly intriguing. Accounting for experimentally known coupling between replisome movement and nucleosome dynamics, we propose a model that can obtain de novo nucleosome assembly similar to what is observed in recent experiments. Simulating nucleosome dynamics during replication, we argue that short pausing of the replication fork, associated with nucleosome disassembly, can be a event crucial for communicating nucleosome positioning information from parent to daughter. We show that the interplay of timescales between nucleosome disassembly (τp) at the replication fork and nucleosome sliding behind the fork (τs) can give rise to a rich ‘phase diagram’ having different inherited patterns of nucleosome organization. Our model predicts that only when τp ≥ τs the daughter chromatin can inherit nucleosome positioning of the parent.
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Affiliation(s)
- Tripti Bameta
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidhyanagari Campus, Mumbai 400098, India
- To whom correspondence should be addressed. Tel: +91 22 25767761; Fax: +91 22 25767760; . Correspondence may also be addressed to Tripti Bameta.
| | - Dibyendu Das
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
- To whom correspondence should be addressed. Tel: +91 22 25767761; Fax: +91 22 25767760; . Correspondence may also be addressed to Tripti Bameta.
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86
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Chereji RV, Clark DJ. Major Determinants of Nucleosome Positioning. Biophys J 2018; 114:2279-2289. [PMID: 29628211 DOI: 10.1016/j.bpj.2018.03.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022] Open
Abstract
The compact structure of the nucleosome limits DNA accessibility and inhibits the binding of most sequence-specific proteins. Nucleosomes are not randomly located on the DNA but positioned with respect to the DNA sequence, suggesting models in which critical binding sites are either exposed in the linker, resulting in activation, or buried inside a nucleosome, resulting in repression. The mechanisms determining nucleosome positioning are therefore of paramount importance for understanding gene regulation and other events that occur in chromatin, such as transcription, replication, and repair. Here, we review our current understanding of the major determinants of nucleosome positioning: DNA sequence, nonhistone DNA-binding proteins, chromatin-remodeling enzymes, and transcription. We outline the major challenges for the future: elucidating the precise mechanisms of chromatin opening and promoter activation, identifying the complexes that occupy promoters, and understanding the multiscale problem of chromatin fiber organization.
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Affiliation(s)
- Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
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87
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Chereji RV, Ramachandran S, Bryson TD, Henikoff S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biol 2018; 19:19. [PMID: 29426353 PMCID: PMC5807854 DOI: 10.1186/s13059-018-1398-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 01/24/2018] [Indexed: 11/10/2022] Open
Abstract
We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our single nucleosome positioning data reveal that nucleosomes occupy preferred positions that differ by integral multiples of the DNA helical repeat. By comparing nucleosome dyad positioning maps to existing genomic and transcriptomic data, we evaluated the contributions of sequence, transcription, and histones H1 and H2A.Z in defining the chromatin landscape. We present a biophysical model that neglects DNA sequence and shows that steric occlusion suffices to explain the salient features of nucleosome positioning.
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Affiliation(s)
- Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Srinivas Ramachandran
- Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Terri D Bryson
- Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
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88
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Barel I, Naughton B, Reich NO, Brown FLH. Specificity versus Processivity in the Sequential Modification of DNA: A Study of DNA Adenine Methyltransferase. J Phys Chem B 2018; 122:1112-1120. [DOI: 10.1021/acs.jpcb.7b10349] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Itay Barel
- Department
of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, United States
- Department
of Physics, University of California, Santa Barbara, California 93106, United States
| | - Brigitte Naughton
- Department
of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, United States
| | - Norbert O. Reich
- Department
of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, United States
| | - Frank L. H. Brown
- Department
of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, United States
- Department
of Physics, University of California, Santa Barbara, California 93106, United States
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89
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Ramachandran S, Henikoff S. MINCE-Seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing. Methods Mol Biol 2018; 1832:159-168. [PMID: 30073526 DOI: 10.1007/978-1-4939-8663-7_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The epigenome has been mapped in different cell types to understand the relationship between the chromatin landscape and the control of gene expression. Most mapping studies profile a large population of cells in various stages of the cell cycle, which results in an average snapshot of the chromatin landscape. However, chromatin is highly dynamic, undergoing rapid changes during active processes such as replication, transcription, repair, and remodeling. Hence, we need methods to map chromatin as a function of time. To address this problem in the context of replication, we developed the method MINCE-seq (Mapping In vivo Nascent Chromatin with EdU and sequencing). MINCE-seq is a genome-wide method that uses the passage of replication fork as a starting point to map the chromatin landscape as a function of time. MINCE-seq can measure chromatin dynamics in a time scale of minutes and at the resolution of individual nucleosome positions and transcription factor-binding sites genome-wide.
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Affiliation(s)
- Srinivas Ramachandran
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, 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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90
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Serra-Cardona A, Zhang Z. Replication-Coupled Nucleosome Assembly in the Passage of Epigenetic Information and Cell Identity. Trends Biochem Sci 2017; 43:136-148. [PMID: 29292063 DOI: 10.1016/j.tibs.2017.12.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 12/31/2022]
Abstract
During S phase, replicated DNA must be assembled into nucleosomes using both newly synthesized and parental histones in a process that is tightly coupled to DNA replication. This DNA replication-coupled process is regulated by multitude of histone chaperones as well as by histone-modifying enzymes. In recent years novel insights into nucleosome assembly of new H3-H4 tetramers have been gained through studies on the classical histone chaperone CAF-1 and the identification of novel factors involved in this process. Moreover, in vitro reconstitution of chromatin replication has shed light on nucleosome assembly of parental H3-H4, a process that remains elusive. Finally, recent studies have revealed that the replication-coupled nucleosome assembly is important for the determination and maintenance of cell fate in multicellular organisms.
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Affiliation(s)
- Albert Serra-Cardona
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Genetics and Development, Columbia University, New York, NY 10032, USA.
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91
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Ramachandran S, Ahmad K, Henikoff S. Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates. Mol Cell 2017; 68:1038-1053.e4. [PMID: 29225036 PMCID: PMC6421108 DOI: 10.1016/j.molcel.2017.11.015] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/29/2017] [Accepted: 11/10/2017] [Indexed: 12/29/2022]
Abstract
Nucleosomes are disrupted during transcription and other active processes, but the structural intermediates during nucleosome disruption in vivo are unknown. To identify intermediates, we mapped subnucleosomal protections in Drosophila cells using Micrococcal Nuclease followed by sequencing. At the first nucleosome position downstream of the transcription start site, we identified unwrapped intermediates, including hexasomes that lack either proximal or distal contacts. Inhibiting topoisomerases or depleting histone chaperones increased unwrapping, whereas inhibiting release of paused RNAPII or reducing RNAPII elongation decreased unwrapping. Our results indicate that positive torsion generated by elongating RNAPII causes transient loss of histone-DNA contacts. Using this mapping approach, we found that nucleosomes flanking human CTCF insulation sites are similarly disrupted. We also identified diagnostic subnucleosomal particle remnants in cell-free human DNA data as a relic of transcribed genes from apoptosing cells. Thus identification of subnucleosomal fragments from nuclease protection data represents a general strategy for structural epigenomics.
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Affiliation(s)
- Srinivas Ramachandran
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, 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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92
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Luo H, Xi Y, Li W, Li J, Li Y, Dong S, Peng L, Liu Y, Yu W. Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle. Hum Mol Genet 2017; 26:4231-4243. [DOI: 10.1093/hmg/ddx312] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/02/2017] [Indexed: 12/29/2022] Open
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93
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Chen T, van Steensel B. Comprehensive analysis of nucleocytoplasmic dynamics of mRNA in Drosophila cells. PLoS Genet 2017; 13:e1006929. [PMID: 28771467 PMCID: PMC5557608 DOI: 10.1371/journal.pgen.1006929] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 08/15/2017] [Accepted: 07/17/2017] [Indexed: 01/14/2023] Open
Abstract
Eukaryotic mRNAs undergo a cycle of transcription, nuclear export, and degradation. A major challenge is to obtain a global, quantitative view of these processes. Here we measured the genome-wide nucleocytoplasmic dynamics of mRNA in Drosophila cells by metabolic labeling in combination with cellular fractionation. By mathematical modeling of these data we determined rates of transcription, export and cytoplasmic decay for 5420 genes. We characterized these kinetic rates and investigated links with mRNA features, RNA-binding proteins (RBPs) and chromatin states. We found prominent correlations between mRNA decay rate and transcript size, while nuclear export rates are linked to the size of the 3'UTR. Transcription, export and decay rates are each associated with distinct spectra of RBPs. Specific classes of genes, such as those encoding cytoplasmic ribosomal proteins, exhibit characteristic combinations of rate constants, suggesting modular control. Binding of splicing factors is associated with faster rates of export, and our data suggest coordinated regulation of nuclear export of specific functional classes of genes. Finally, correlations between rate constants suggest global coordination between the three processes. Our approach provides insights into the genome-wide nucleocytoplasmic kinetics of mRNA and should be generally applicable to other cell systems. All mRNAs start from production in the nucleus, undergo exportation through nuclear pores and finally are degraded in the cytoplasm. A comprehensive characterization of the kinetic rates of all mRNAs is an important prerequisite for a global understanding of the regulation of the transcriptome and the cell. By conducting a time-series experiment and building a mathematical model, we trace the dynamics of mRNAs from the nucleus to the cytoplasm and determine the rates at each kinetic step at transcriptome-wide level. This information allows us to associate mRNA kinetic rates with a wealth of biological features and made some intriguing discoveries. We show mRNA decay is positively linked to transcript length while mRNA export is negatively linked to the length of the 3' UTR. We show binding of splicing factors is associated with faster rates of mRNA export. We provide evidence for global coordination between nuclear export an decay of mRNA. We show genes sharing specific functions tend to have similar nucleoplasmic kinetics, in which ribosomal proteins possessing special kinetic features exclusively stand out. Altogether, our integrated approach to quantitatively determine the rates of kinetic steps on a gene-by-gene basis provides a blueprint to obtain the global understanding of RNA regulation.
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Affiliation(s)
- Tao Chen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail:
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94
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The Effects of Replication Stress on S Phase Histone Management and Epigenetic Memory. J Mol Biol 2017; 429:2011-2029. [DOI: 10.1016/j.jmb.2016.11.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 12/14/2022]
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95
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Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nat Rev Mol Cell Biol 2017; 18:548-562. [PMID: 28537572 DOI: 10.1038/nrm.2017.47] [Citation(s) in RCA: 298] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in genomics technology have provided the means to probe myriad chromatin interactions at unprecedented spatial and temporal resolution. This has led to a profound understanding of nucleosome organization within the genome, revealing that nucleosomes are highly dynamic. Nucleosome dynamics are governed by a complex interplay of histone composition, histone post-translational modifications, nucleosome occupancy and positioning within chromatin, which are influenced by numerous regulatory factors, including general regulatory factors, chromatin remodellers, chaperones and polymerases. It is now known that these dynamics regulate diverse cellular processes ranging from gene transcription to DNA replication and repair.
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96
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Cuvier O, Fierz B. Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells. Nat Rev Genet 2017; 18:457-472. [DOI: 10.1038/nrg.2017.28] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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97
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Wyse B, Oshidari R, Rowlands H, Abbasi S, Yankulov K. RRM3 regulates epigenetic conversions in Saccharomyces cerevisiae in conjunction with Chromatin Assembly Factor I. Nucleus 2017; 7:405-14. [PMID: 27645054 DOI: 10.1080/19491034.2016.1212796] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Chromatin structures are transmitted to daughter cells through a complex system of nucleosome disassembly and re-assembly at the advancing replication forks. However, the role of replication pausing in the transmission and perturbation of chromatin structures has not been addressed. RRM3 encodes a DNA helicase, which facilitates replication at sites covered with non-histone protein complexes (tRNA genes, active gene promoters, telomeres) in Saccharomyces cerevisiae. In this report we show that the deletion of RRM3 reduces the frequency of epigenetic conversions in the subtelomeric regions of the chromosomes. This phenotype is strongly dependent on 2 histone chaperones, CAF-I and ASF1, which are involved in the reassembly of nucleosomes behind replication forks, but not on the histone chaperone HIR1. We also show that the deletion of RRM3 increases the spontaneous mutation rates in conjunction with CAF-I and ASF1, but not HIR1. Finally, we demonstrate that Rrm3p and CAF-I compete for the binding to the DNA replication clamp PCNA (Proliferating Cell Nuclear Antigen). We propose that the stalling of DNA replication predisposes to epigenetic conversions and that RRM3 and CAF-I play key roles in this process.
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Affiliation(s)
- Brandon Wyse
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
| | - Roxanne Oshidari
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
| | - Hollie Rowlands
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
| | - Sanna Abbasi
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
| | - Krassimir Yankulov
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
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98
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Joseph SR, Pálfy M, Hilbert L, Kumar M, Karschau J, Zaburdaev V, Shevchenko A, Vastenhouw NL. Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos. eLife 2017; 6. [PMID: 28425915 PMCID: PMC5451213 DOI: 10.7554/elife.23326] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/19/2017] [Indexed: 01/09/2023] Open
Abstract
Upon fertilization, the genome of animal embryos remains transcriptionally inactive until the maternal-to-zygotic transition. At this time, the embryo takes control of its development and transcription begins. How the onset of zygotic transcription is regulated remains unclear. Here, we show that a dynamic competition for DNA binding between nucleosome-forming histones and transcription factors regulates zebrafish genome activation. Taking a quantitative approach, we found that the concentration of non-DNA-bound core histones sets the time for the onset of transcription. The reduction in nuclear histone concentration that coincides with genome activation does not affect nucleosome density on DNA, but allows transcription factors to compete successfully for DNA binding. In agreement with this, transcription factor binding is sensitive to histone levels and the concentration of transcription factors also affects the time of transcription. Our results demonstrate that the relative levels of histones and transcription factors regulate the onset of transcription in the embryo. DOI:http://dx.doi.org/10.7554/eLife.23326.001 The DNA in a fertilized egg contains all the information required to form an animal’s body. In order for the animal to develop properly, particular genes encoded in the DNA are only active at specific times. The DNA is wrapped around proteins called histones, which allows the DNA to be tightly packed inside the cell. However, histones can block other proteins called transcription factors from binding to the DNA to activate the genes. Young embryos initially develop with all of their genes switched off, relying on the nutrients and other molecules provided by their mother. After some time, the embryo starts to switch on its own genes to take control of its own development, but it was not clear how this happens. Joseph et al. investigated how genes are activated in zebrafish embryos, which are often used as models to study how animals develop. The experiments show that competition between histones and transcription factors for binding to DNA controls when genes are switched on. In young fish embryos, there are so many histones present that transcription factors have no opportunity to bind to DNA. Over time, however, the numbers of histones decrease, allowing transcription factors to bind to DNA and switch on genes. Histones and transcription factors regulate the activity of genes throughout the life of the animal. Therefore, competition between these two types of protein may also control gene activity in other situations. A better understanding of how gene activity is controlled could allow researchers to more easily grow different types of cell in the laboratory or to reprogram specific cells in the body. As such, these new findings may aid the development of therapies to regenerate organs or tissues that have been damaged by injury or disease. DOI:http://dx.doi.org/10.7554/eLife.23326.002
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Affiliation(s)
- Shai R Joseph
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Máté Pálfy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Lennart Hilbert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Mukesh Kumar
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jens Karschau
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Vasily Zaburdaev
- Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Andrej Shevchenko
- 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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99
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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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100
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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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