1
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Kain J, Wei X, Reddy NA, Price AJ, Woods C, Bochkis IM. Pioneer factor Foxa2 enables ligand-dependent activation of type II nuclear receptors FXR and LXRα. Mol Metab 2021; 53:101291. [PMID: 34246806 PMCID: PMC8350412 DOI: 10.1016/j.molmet.2021.101291] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
Objective Type II nuclear hormone receptors, including farnesoid X receptors (FXR), liver X receptors (LXR), and peroxisome proliferator-activated receptors (PPAR), which serve as drug targets for metabolic diseases, are permanently positioned in the nucleus and thought to be bound to DNA regardless of the ligand status. However, recent genome-wide location analysis showed that LXRα and PPARα binding in the liver is largely ligand-dependent. We hypothesized that pioneer factor Foxa2 evicts nucleosomes to enable ligand-dependent binding of type II nuclear receptors and performed genome-wide studies to test this hypothesis. Methods ATAC-Seq was used to profile chromatin accessibility; ChIP-Seq was performed to assess transcription factors (Foxa2, FXR, LXRα, and PPARα) binding; and RNA-Seq analysis determined differentially expressed genes in wildtype and Foxa2 mutants treated with a ligand (GW4064 for FXR, GW3965, and T09 for LXRα). Results We reveal that chromatin accessibility, FXR binding, LXRα occupancy, and ligand-responsive activation of gene expression by FXR and LXRα require Foxa2. Unexpectedly, Foxa2 occupancy is drastically increased when either receptor, FXR or LXRα, is bound by an agonist. In addition, co-immunoprecipitation experiments demonstrate that Foxa2 interacts with either receptor in a ligand-dependent manner, suggesting that Foxa2 and the receptor, bind DNA as an interdependent complex during ligand activation. Furthermore, PPARα binding is induced in Foxa2 mutants treated with FXR and LXR ligands, leading to the activation of PPARα targets. Conclusions Our model requires pioneering activity for ligand activation that challenges the existing ligand-independent binding mechanism. We also demonstrate that Foxa2 is required to achieve activation of the proper receptor – one that binds the added ligand – by repressing the activity of a competing receptor. Foxa2 opens chromatin for FXR and LXRα binding during acute ligand activation. Ligand-dependent activation of FXR & LXR-dependent gene expression requires Foxa2. Foxa2 interacts with FXR and LXRα in a ligand-dependent manner. Foxa2 restricts binding of competing receptor PPARα to ensure proper ligand-dependent activation of FXR and LXRα.
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Affiliation(s)
- Jessica Kain
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Xiaolong Wei
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Nihal A Reddy
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Andrew J Price
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Claire Woods
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Irina M Bochkis
- Department of Pharmacology, University of Virginia, Charlottesville, VA, 22908, USA.
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2
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Martínez-García PM, García-Torres M, Divina F, Terrón-Bautista J, Delgado-Sainz I, Gómez-Vela F, Cortés-Ledesma F. Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility. PLoS Comput Biol 2021; 17:e1007814. [PMID: 33465072 PMCID: PMC7845959 DOI: 10.1371/journal.pcbi.1007814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 01/29/2021] [Accepted: 11/13/2020] [Indexed: 12/28/2022] Open
Abstract
DNA topoisomerase II-β (TOP2B) is fundamental to remove topological problems linked to DNA metabolism and 3D chromatin architecture, but its cut-and-reseal catalytic mechanism can accidentally cause DNA double-strand breaks (DSBs) that can seriously compromise genome integrity. Understanding the factors that determine the genome-wide distribution of TOP2B is therefore not only essential for a complete knowledge of genome dynamics and organization, but also for the implications of TOP2-induced DSBs in the origin of oncogenic translocations and other types of chromosomal rearrangements. Here, we conduct a machine-learning approach for the prediction of TOP2B binding using publicly available sequencing data. We achieve highly accurate predictions, with accessible chromatin and architectural factors being the most informative features. Strikingly, TOP2B is sufficiently explained by only three features: DNase I hypersensitivity, CTCF and cohesin binding, for which genome-wide data are widely available. Based on this, we develop a predictive model for TOP2B genome-wide binding that can be used across cell lines and species, and generate virtual probability tracks that accurately mirror experimental ChIP-seq data. Our results deepen our knowledge on how the accessibility and 3D organization of chromatin determine TOP2B function, and constitute a proof of principle regarding the in silico prediction of sequence-independent chromatin-binding factors.
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Affiliation(s)
- Pedro Manuel Martínez-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
- * E-mail: (PMMG); (FCL)
| | | | - Federico Divina
- Division of Computer Science, Universidad Pablo de Olavide, Seville, Spain
| | - José Terrón-Bautista
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| | - Irene Delgado-Sainz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| | | | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
- Topology and DNA breaks Group, Spanish National Cancer Centre (CNIO), Madrid, Spain
- * E-mail: (PMMG); (FCL)
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3
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Papin C, Le Gras S, Ibrahim A, Salem H, Karimi MM, Stoll I, Ugrinova I, Schröder M, Fontaine-Pelletier E, Omran Z, Bronner C, Dimitrov S, Hamiche A. CpG Islands Shape the Epigenome Landscape. J Mol Biol 2020; 433:166659. [PMID: 33010306 DOI: 10.1016/j.jmb.2020.09.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
Epigenetic modifications and nucleosome positioning play an important role in modulating gene expression. However, how the patterns of epigenetic modifications and nucleosome positioning are established around promoters is not well understood. Here, we have addressed these questions in a series of genome-wide experiments coupled to a novel bioinformatic analysis approach. Our data reveal a clear correlation between CpG density, promoter activity and accumulation of active or repressive histone marks. CGI boundaries define the chromatin promoter regions that will be epigenetically modified. CpG-rich promoters are targeted by histone modifications and histone variants, while CpG-poor promoters are regulated by DNA methylation. CGIs boundaries, but not transcriptional activity, are essential determinants of H2A.Z positioning in vicinity of the promoters, suggesting that the presence of H2A.Z is not related to transcriptional control. Accordingly, H2A.Z depletion has no impact on gene expression of arrested mouse embryonic fibroblasts. Therefore, the underlying DNA sequence, the promoter CpG density and, to a lesser extent, transcriptional activity, are key factors implicated in promoter chromatin architecture.
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Affiliation(s)
- Christophe Papin
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142,67404 Illkirch Cedex, France.
| | - Stéphanie Le Gras
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142,67404 Illkirch Cedex, France
| | - Abdulkhaleg Ibrahim
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142,67404 Illkirch Cedex, France; Biotechnology Research Center (BTRC), Tripoli, Libya
| | - Hatem Salem
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142,67404 Illkirch Cedex, France; Biotechnology Research Center (BTRC), Tripoli, Libya
| | - Mohammad Mahdi Karimi
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, Denmark Hill, London, UK
| | - Isabelle Stoll
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142,67404 Illkirch Cedex, France
| | - Iva Ugrinova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Schröder
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Emeline Fontaine-Pelletier
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Ziad Omran
- Umm AlQura University, Faculty of Pharmacy, Saudi Arabia
| | - Christian Bronner
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142,67404 Illkirch Cedex, France
| | - Stefan Dimitrov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria; Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France.
| | - Ali Hamiche
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142,67404 Illkirch Cedex, France.
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4
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Macchi F, Sadler KC. Unraveling the Epigenetic Basis of Liver Development, Regeneration and Disease. Trends Genet 2020; 36:587-597. [PMID: 32487496 DOI: 10.1016/j.tig.2020.05.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Abstract
A wealth of studies over several decades has revealed an epigenetic prepattern that determines the competence of cellular differentiation in the developing liver. More recently, studies focused on the impact of epigenetic factors during liver regeneration suggest that an epigenetic code in the quiescent liver may establish its regenerative potential. We review work on the pioneer factors and other chromatin remodelers that impact the gene expression patterns instructing hepatocyte and biliary cell specification and differentiation, along with the requirement of epigenetic regulatory factors for hepatic outgrowth. We then explore recent studies involving the role of epigenetic regulators, Arid1a and Uhrf1, in efficient activation of proregenerative genes during liver regeneration, thus highlighting the epigenetic mechanisms of liver disease and tumor development.
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Affiliation(s)
- Filippo Macchi
- Program in Biology, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Kirsten C Sadler
- Program in Biology, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
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5
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Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones. Nat Genet 2020; 52:418-427. [PMID: 32203463 PMCID: PMC7901023 DOI: 10.1038/s41588-020-0591-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/14/2020] [Indexed: 12/17/2022]
Abstract
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. But a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short alpha-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.
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6
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Oruba A, Saccani S, van Essen D. Role of cell-type specific nucleosome positioning in inducible activation of mammalian promoters. Nat Commun 2020; 11:1075. [PMID: 32103026 PMCID: PMC7044431 DOI: 10.1038/s41467-020-14950-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/10/2020] [Indexed: 12/18/2022] Open
Abstract
The organization of nucleosomes across functional genomic elements represents a critical layer of control. Here, we present a strategy for high-resolution nucleosome profiling at selected genomic features, and use this to analyse dynamic nucleosome positioning at inducible and cell-type-specific mammalian promoters. We find that nucleosome patterning at inducible promoters frequently resembles that at active promoters, even before stimulus-driven activation. Accordingly, the nucleosome profile at many inactive inducible promoters is sufficient to predict cell-type-specific responsiveness. Induction of gene expression is generally not associated with major changes to nucleosome patterning, and a subset of inducible promoters can be activated without stable nucleosome depletion from their transcription start sites. These promoters are generally dependent on remodelling enzymes for their inducible activation, and exhibit transient nucleosome depletion only at alleles undergoing transcription initiation. Together, these data reveal how the responsiveness of inducible promoters to activating stimuli is linked to cell-type-specific nucleosome patterning. Nucleosome organisation plays important roles in regulating functional genomic elements. Here, the authors use high-resolution profiling to analyse dynamic nucleosome positioning at inducible and cell-type-specific promoters, providing a global view of chromatin architecture at inducible promoters.
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Affiliation(s)
- Agata Oruba
- Max Planck Institute for Immunobiology & Epigenetics, Stübeweg 51, Freiburg, D79108, Germany
| | - Simona Saccani
- Max Planck Institute for Immunobiology & Epigenetics, Stübeweg 51, Freiburg, D79108, Germany. .,Institute for Research on Cancer & Aging, Nice (IRCAN), 28 Avenue Valombrose, Nice, 06107, France.
| | - Dominic van Essen
- Max Planck Institute for Immunobiology & Epigenetics, Stübeweg 51, Freiburg, D79108, Germany. .,Institute for Research on Cancer & Aging, Nice (IRCAN), 28 Avenue Valombrose, Nice, 06107, France.
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7
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Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression. Immunity 2020; 52:257-274.e11. [PMID: 32049053 DOI: 10.1016/j.immuni.2020.01.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/23/2019] [Accepted: 01/15/2020] [Indexed: 02/06/2023]
Abstract
Genetics is a major determinant of susceptibility to autoimmune disorders. Here, we examined whether genome organization provides resilience or susceptibility to sequence variations, and how this would contribute to the molecular etiology of an autoimmune disease. We generated high-resolution maps of linear and 3D genome organization in thymocytes of NOD mice, a model of type 1 diabetes (T1D), and the diabetes-resistant C57BL/6 mice. Multi-enhancer interactions formed at genomic regions harboring genes with prominent roles in T cell development in both strains. However, diabetes risk-conferring loci coalesced enhancers and promoters in NOD, but not C57BL/6 thymocytes. 3D genome mapping of NODxC57BL/6 F1 thymocytes revealed that genomic misfolding in NOD mice is mediated in cis. Moreover, immune cells infiltrating the pancreas of humans with T1D exhibited increased expression of genes located on misfolded loci in mice. Thus, genetic variation leads to altered 3D chromatin architecture and associated changes in gene expression that may underlie autoimmune pathology.
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8
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Karagianni P, Moulos P, Schmidt D, Odom DT, Talianidis I. Bookmarking by Non-pioneer Transcription Factors during Liver Development Establishes Competence for Future Gene Activation. Cell Rep 2020; 30:1319-1328.e6. [PMID: 32023452 PMCID: PMC7003066 DOI: 10.1016/j.celrep.2020.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/02/2019] [Accepted: 12/31/2019] [Indexed: 01/01/2023] Open
Abstract
Transcription factor binding to enhancer and promoter regions critical for homeostatic adult gene activation is established during development. To understand how cell-specific gene expression patterns are generated, we study the developmental timing of association of two prominent hepatic transcription factors with gene regulatory regions. Most individual binding events display extraordinarily high temporal variations during liver development. Early and persistent binding is necessary, but not sufficient, for gene activation. Stable gene expression patterns are the result of combinatorial activity of multiple transcription factors, which mark regulatory regions long before activation and promote progressive broadening of active chromatin domains. Both temporally stable and dynamic, short-lived binding events contribute to the developmental maturation of active promoter configurations. The results reveal a developmental bookmarking function of master regulators and illuminate remarkable parallels between the principles employed for gene activation during development, during evolution, and upon mitotic exit.
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Affiliation(s)
- Panagiota Karagianni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Herakleion, Crete, Greece; Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece
| | - Panagiotis Moulos
- Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece
| | - Dominic Schmidt
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Duncan T Odom
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Iannis Talianidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Herakleion, Crete, Greece.
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9
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Chen Y, Bravo JI, Son JM, Lee C, Benayoun BA. Remodeling of the H3 nucleosomal landscape during mouse aging. TRANSLATIONAL MEDICINE OF AGING 2020; 4:22-31. [PMID: 32462102 DOI: 10.1016/j.tma.2019.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and deregulation of gene expression correlates with aging. A key layer in the study of gene regulation mechanisms lies at the level of chromatin: cellular chromatin states (i.e. the 'epigenome') can tune transcriptional profiles, and, in line with the prevalence of transcriptional alterations with aging, accumulating evidence suggests that the chromatin landscape is altered with aging across cell types and species. However, although alterations in the chromatin make-up of cells are considered to be a hallmark of aging, little is known of the genomic loci that are specifically affected by age-related chromatin state remodeling and of their biological significance. Here, we report the analysis of genome-wide profiles of core histone H3 occupancy in aging male mouse tissues (i.e. heart, liver, cerebellum and olfactory bulb) and primary cultures of neural stem cells. We find that, although no drastic changes in H3 levels are observed, local changes in H3 occupancy occur with aging across tissues and cells with both regions of increased or decreased occupancy. These changes are compatible with a general increase in chromatin accessibility at pro-inflammatory genes and may thus mechanistically underlie known shift in gene expression programs during aging.
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Affiliation(s)
- Yilin Chen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,Master of Science in Nutrition, Healthspan, and Longevity, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Jyung Mean Son
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA.,Biomedical Sciences, Graduate School, Ajou University, Suwon 16499, Republic of Korea
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA.,USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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10
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Zheng D, Trynda J, Sun Z, Li Z. NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions. BMC Genomics 2019; 20:541. [PMID: 31266464 PMCID: PMC6604165 DOI: 10.1186/s12864-019-5932-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/24/2019] [Indexed: 01/06/2023] Open
Abstract
Background Defining histone modification at single-nucleosome resolution provides accurate epigenomic information in individual nucleosomes. However, most of histone modification data deposited in current databases, such as ENCODE and Roadmap, have low resolution with peaks of several kilo-base pairs (kb), which due to the technical defects of regular ChIP-Seq technology. Results To generate histone modification data at single-nucleosome resolution, we developed a novel approach, NUCLIZE, using synergistic analyses of histone modification data from ChIP-Seq and high-resolution nucleosome mapping data from native MNase-Seq. With this approach, we generated quantitative epigenomics data of single and multivalent histone modification marks in each nucleosome. We found that the dominant trivalent histone mark (H3K4me3/H3K9ac/H3K27ac) and others showed defined and specific patterns near each TSS, indicating potential epigenetic codes regulating gene transcription. Conclusions Single-nucleosome histone modification data render epigenomic data become quantitative, which is essential for investigating dynamic changes of epigenetic regulation in the biological process or for functional epigenomics studies. Thus, NUCLIZE turns current epigenomic mapping studies into genuine functional epigenomics studies with quantitative epigenomic data. Electronic supplementary material The online version of this article (10.1186/s12864-019-5932-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daoshan Zheng
- Department of Cancer Biology and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Griffin 210, Jacksonville, FL, 32224, USA
| | - Justyna Trynda
- Department of Cancer Biology and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Griffin 210, Jacksonville, FL, 32224, USA
| | - Zhifu Sun
- Bioinformatics Core and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Griffin 210, Jacksonville, FL, 32224, USA
| | - Zhaoyu Li
- Department of Cancer Biology and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Griffin 210, Jacksonville, FL, 32224, USA.
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11
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Ren J, Finney R, Ni K, Cam M, Muegge K. The chromatin remodeling protein Lsh alters nucleosome occupancy at putative enhancers and modulates binding of lineage specific transcription factors. Epigenetics 2019; 14:277-293. [PMID: 30861354 PMCID: PMC6557562 DOI: 10.1080/15592294.2019.1582275] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/07/2019] [Accepted: 02/07/2019] [Indexed: 12/12/2022] Open
Abstract
Dynamic regulation of chromatin accessibility is a key feature of cellular differentiation during embryogenesis, but the precise factors that control access to chromatin remain largely unknown. Lsh/HELLS is critical for normal development and mutations of Lsh in human cause the ICF (Immune deficiency, Centromeric instability, Facial anomalies) syndrome, a severe immune disorder with multiple organ deficiencies. We report here that Lsh, previously known to regulate DNA methylation level, has a genome wide chromatin remodeling function. Using micrococcal nuclease (MNase)-seq analysis, we demonstrate that Lsh protects MNase accessibility at transcriptional regulatory regions characterized by DNase I hypersensitivity and certain histone 3 (H3) tail modifications associated with enhancers. Using an auxin-inducible degron system, allowing proteolytical degradation of Lsh, we show that Lsh mediated changes in nucleosome occupancy are independent of DNA methylation level and are characterized by reduced H3 occupancy. While Lsh mediated nucleosome occupancy prevents binding sites for transcription factors in wild type cells, depletion of Lsh leads to an increase in binding of ectopically expressed tissue specific transcription factors to their respective binding sites. Our data suggests that Lsh mediated chromatin remodeling can modulate nucleosome positioning at a subset of putative enhancers contributing to the preservation of cellular identity through regulation of accessibility.
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Affiliation(s)
- Jianke Ren
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Richard Finney
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kai Ni
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
- Frederick National Laboratory for Cancer Research, Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, USA
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12
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Abstract
The essential liver exocrine and endocrine functions require a precise spatial arrangement of the hepatic lobule consisting of the central vein, portal vein, hepatic artery, intrahepatic bile duct system, and hepatocyte zonation. This allows blood to be carried through the liver parenchyma sampled by all hepatocytes and bile produced by the hepatocytes to be carried out of the liver through the intrahepatic bile duct system composed of cholangiocytes. The molecular orchestration of multiple signaling pathways and epigenetic factors is required to set up lineage restriction of the bipotential hepatoblast progenitor into the hepatocyte and cholangiocyte cell lineages, and to further refine cell fate heterogeneity within each cell lineage reflected in the functional heterogeneity of hepatocytes and cholangiocytes. In addition to the complex molecular regulation, there is a complicated morphogenetic choreography observed in building the refined hepatic epithelial architecture. Given the multifaceted molecular and cellular regulation, it is not surprising that impairment of any of these processes can result in acute and chronic hepatobiliary diseases. To enlighten the development of potential molecular and cellular targets for therapeutic options, an understanding of how the intricate hepatic molecular and cellular interactions are regulated is imperative. Here, we review the signaling pathways and epigenetic factors regulating hepatic cell lineages, fates, and epithelial architecture.
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Affiliation(s)
- Stacey S Huppert
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
| | - Makiko Iwafuchi-Doi
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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13
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Ye C, Chen M, Chen E, Li W, Wang S, Ding Q, Wang C, Zhou C, Tang L, Hou W, Hang K, He R, Pan Z, Zhang W. Knockdown of FOXA2 enhances the osteogenic differentiation of bone marrow-derived mesenchymal stem cells partly via activation of the ERK signalling pathway. Cell Death Dis 2018; 9:836. [PMID: 30082727 PMCID: PMC6079048 DOI: 10.1038/s41419-018-0857-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/26/2018] [Accepted: 07/05/2018] [Indexed: 02/07/2023]
Abstract
Forkhead box protein A2 (FOXA2) is a core transcription factor that controls cell differentiation and may have an important role in bone metabolism. However, the role of FOXA2 during osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs) remains largely unknown. In this study, decreased expression of FOXA2 was observed during osteogenic differentiation of rat BMSCs (rBMSCs). FOXA2 knockdown significantly increased osteoblast-specific gene expression, the number of mineral deposits and alkaline phosphatase activity, whereas FOXA2 overexpression inhibited osteogenesis-specific activities. Moreover, extracellular signal-regulated protein kinase (ERK) signalling was upregulated following knockdown of FOXA2. The enhanced osteogenesis due to FOXA2 knockdown was partially rescued by an ERK inhibitor. Using a rat tibial defect model, a rBMSC sheet containing knocked down FOXA2 significantly improved bone healing. Collectively, these findings indicated that FOXA2 had an essential role in osteogenic differentiation of BMSCs, partly by activation of the ERK signalling pathway.
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Affiliation(s)
- Chenyi Ye
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Mo Chen
- Department of Rheumatology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Erman Chen
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Weixu Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Shengdong Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Qianhai Ding
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Cong Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Chenhe Zhou
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Lan Tang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Weiduo Hou
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Kai Hang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China
| | - Rongxin He
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China. .,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.
| | - Zhijun Pan
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China. .,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.
| | - Wei Zhang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China. .,Orthopedics Research Institute of Zhejiang University, No. 88, Jiefang Road, Hangzhou, 310009, China.
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14
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Whitton H, Singh LN, Patrick MA, Price AJ, Osorio FG, López‐Otín C, Bochkis IM. Changes at the nuclear lamina alter binding of pioneer factor Foxa2 in aged liver. Aging Cell 2018; 17:e12742. [PMID: 29484800 PMCID: PMC5946061 DOI: 10.1111/acel.12742] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2018] [Indexed: 12/23/2022] Open
Abstract
Increasing evidence suggests that regulation of heterochromatin at the nuclear envelope underlies metabolic disease susceptibility and age-dependent metabolic changes, but the mechanism is unknown. Here, we profile lamina-associated domains (LADs) using lamin B1 ChIP-Seq in young and old hepatocytes and find that, although lamin B1 resides at a large fraction of domains at both ages, a third of lamin B1-associated regions are bound exclusively at each age in vivo. Regions occupied by lamin B1 solely in young livers are enriched for the forkhead motif, bound by Foxa pioneer factors. We also show that Foxa2 binds more sites in Zmpste24 mutant mice, a progeroid laminopathy model, similar to increased Foxa2 occupancy in old livers. Aged and Zmpste24-deficient livers share several features, including nuclear lamina abnormalities, increased Foxa2 binding, de-repression of PPAR- and LXR-dependent gene expression, and fatty liver. In old livers, additional Foxa2 binding is correlated to loss of lamin B1 and heterochromatin (H3K9me3 occupancy) at these loci. Our observations suggest that changes at the nuclear lamina are linked to altered Foxa2 binding, enabling opening of chromatin and de-repression of genes encoding lipid synthesis and storage targets that contribute to etiology of hepatic steatosis.
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Affiliation(s)
| | - Larry N. Singh
- Center for Mitochondrial and Epigenomic MedicineChildren's Hospital of PhiladelphiaPhiladelphiaPAUSA
| | | | - Andrew J. Price
- Department of PharmacologyUniversity of VirginiaCharlottesvilleVAUSA
| | - Fernando G. Osorio
- Departamento de Bioquímica y Biología MolecularFacultad de MedicinaInstituto Universitario de Oncología (IUOPA)Universidad de OviedoOviedoSpain
| | - Carlos López‐Otín
- Departamento de Bioquímica y Biología MolecularFacultad de MedicinaInstituto Universitario de Oncología (IUOPA)Universidad de OviedoOviedoSpain
- Centro de Investigación Biomédica en Red de CáncerMadridSpain
| | - Irina M. Bochkis
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Department of PharmacologyUniversity of VirginiaCharlottesvilleVAUSA
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15
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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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16
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Abstract
Pioneer transcription factors have the unique and important role of unmasking chromatin domains during development to allow the implementation of new cellular programs. Compared with those of other transcription factors, this activity implies that pioneer factors can recognize their target DNA sequences in so-called compacted or "closed" heterochromatin and can trigger remodeling of the adjoining chromatin landscape to provide accessibility to nonpioneer transcription factors. Recent studies identified several steps of pioneer action, namely rapid but weak initial binding to heterochromatin and stabilization of binding followed by chromatin opening and loss of cytosine-phosphate-guanine (CpG) methylation that provides epigenetic memory. Whereas CpG demethylation depends on replication, chromatin opening does not. In this Minireview, we highlight the unique properties of this transcription factor class and the challenges of understanding their mechanism of action.
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Affiliation(s)
- Alexandre Mayran
- From the Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Quebec H2W 1R7, Canada
| | - Jacques Drouin
- From the Laboratory of Molecular Genetics, Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Quebec H2W 1R7, Canada
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17
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Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nat Genet 2018; 50:250-258. [PMID: 29358654 PMCID: PMC6517675 DOI: 10.1038/s41588-017-0034-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 12/04/2017] [Indexed: 12/27/2022]
Abstract
Transcription factors are the core drivers of gene regulatory networks that control developmental transitions, therefore a more complete understanding of how they access, alter and maintain tissue-specific gene expression patterns remains an important goal. To systematically dissect molecular components that enable or constrain their activity, we investigated the genomic occupancy of FOXA2, GATA4 and OCT4 in several cell types. Despite a classification as pioneer factors, all three factors demonstrate cell type specific enrichment even under super-physiological expression. However, only FOXA2 and GATA4 display, in both endogenous and ectopic conditions, a low enrichment sampling of additional loci that are occupied in alternative cell types. Co-factor expression can lead to increased pioneer factor binding at subsets of previously sampled target sites. Finally, we demonstrate that FOXA2 occupancy and changes to DNA accessibility at silent cis-regulatory elements can occur when the cell cycle is halted in G1, but subsequent loss of DNA methylation requires DNA replication.
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18
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Voong LN, Xi L, Wang JP, Wang X. Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping. Trends Genet 2017; 33:495-507. [PMID: 28693826 DOI: 10.1016/j.tig.2017.05.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/10/2017] [Accepted: 05/30/2017] [Indexed: 12/30/2022]
Abstract
Nucleosomes regulate the transcription output of the genome by occluding the underlying DNA sequences from DNA-binding proteins that must act on it. Knowledge of the precise locations of nucleosomes in the genome is thus essential towards understanding how transcription is regulated. Current nucleosome-mapping strategies involve digesting chromatin with nucleases or chemical cleavage followed by high-throughput sequencing. In this review, we compare the traditional micrococcal nuclease (MNase)-based approach with a chemical cleavage strategy, with discussion on the important insights each has uncovered about the role of nucleosomes in shaping transcriptional processes.
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Affiliation(s)
- Lilien N Voong
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Liqun Xi
- Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, IL 60208, USA.
| | - Xiaozhong Wang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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19
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Julian LM, McDonald AC, Stanford WL. Direct reprogramming with SOX factors: masters of cell fate. Curr Opin Genet Dev 2017; 46:24-36. [PMID: 28662445 DOI: 10.1016/j.gde.2017.06.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/25/2017] [Accepted: 06/09/2017] [Indexed: 12/13/2022]
Abstract
Over the last decade significant advances have been made toward reprogramming the fate of somatic cells, typically by overexpression of cell lineage-determinant transcription factors. As key regulators of cell fate, the SOX family of transcription factors has emerged as potent drivers of direct somatic cell reprogramming into multiple lineages, in some cases as the sole overexpressed factor. The vast capacity of SOX factors, especially those of the SOXB1, E and F subclasses, to reprogram cell fate is enlightening our understanding of organismal development, cancer and disease, and offers tremendous potential for regenerative medicine and cell-based therapies. Understanding the molecular mechanisms through which SOX factors reprogram cell fate is essential to optimize the development of novel somatic cell transdifferentiation strategies.
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Affiliation(s)
- Lisa M Julian
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1L8L6, Canada
| | - Angela Ch McDonald
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G0A4, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S3G9, Canada
| | - William L Stanford
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1L8L6, Canada; Department of Cellular and Molecular Medicine, Faulty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H8M5, Canada; Department of Biochemistry, Microbiology and Immunology, Faulty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H8M5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario K1H8M5, Canada.
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20
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Abstract
Forkhead box (Fox) transcription factors are evolutionarily conserved in organisms ranging from yeast to humans. They regulate diverse biological processes both during development and throughout adult life. Mutations in many Fox genes are associated with human disease and, as such, various animal models have been generated to study the function of these transcription factors in mechanistic detail. In many cases, the absence of even a single Fox transcription factor is lethal. In this Primer, we provide an overview of the Fox family, highlighting several key Fox transcription factor families that are important for mammalian development.
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Affiliation(s)
- Maria L Golson
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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Uusküla-Reimand L, Hou H, Samavarchi-Tehrani P, Rudan MV, Liang M, Medina-Rivera A, Mohammed H, Schmidt D, Schwalie P, Young EJ, Reimand J, Hadjur S, Gingras AC, Wilson MD. Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders. Genome Biol 2016; 17:182. [PMID: 27582050 PMCID: PMC5006368 DOI: 10.1186/s13059-016-1043-8] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 08/10/2016] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Type II DNA topoisomerases (TOP2) regulate DNA topology by generating transient double stranded breaks during replication and transcription. Topoisomerase II beta (TOP2B) facilitates rapid gene expression and functions at the later stages of development and differentiation. To gain new insight into the genome biology of TOP2B, we used proteomics (BioID), chromatin immunoprecipitation, and high-throughput chromosome conformation capture (Hi-C) to identify novel proximal TOP2B protein interactions and characterize the genomic landscape of TOP2B binding at base pair resolution. RESULTS Our human TOP2B proximal protein interaction network included members of the cohesin complex and nucleolar proteins associated with rDNA biology. TOP2B associates with DNase I hypersensitivity sites, allele-specific transcription factor (TF) binding, and evolutionarily conserved TF binding sites on the mouse genome. Approximately half of all CTCF/cohesion-bound regions coincided with TOP2B binding. Base pair resolution ChIP-exo mapping of TOP2B, CTCF, and cohesin sites revealed a striking structural ordering of these proteins along the genome relative to the CTCF motif. These ordered TOP2B-CTCF-cohesin sites flank the boundaries of topologically associating domains (TADs) with TOP2B positioned externally and cohesin internally to the domain loop. CONCLUSIONS TOP2B is positioned to solve topological problems at diverse cis-regulatory elements and its occupancy is a highly ordered and prevalent feature of CTCF/cohesin binding sites that flank TADs.
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Affiliation(s)
- Liis Uusküla-Reimand
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON Canada
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Huayun Hou
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | | | - Matteo Vietri Rudan
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Minggao Liang
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Alejandra Medina-Rivera
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON Canada
- Present address: International Laboratory for Research in Human Genomics, Universidad Nacional Autónoma de México, Juriquilla, Querétaro Mexico
| | - Hisham Mohammed
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
- Present address: The Babraham Institute, Cambridge, UK
| | - Dominic Schmidt
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
- Present address: Syncona Partners LLP, London, UK
| | - Petra Schwalie
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- Present address: Laboratory of Systems Biology and Genetics, Lausanne, Switzerland
| | - Edwin J. Young
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON Canada
| | - Jüri Reimand
- Ontario Institute for Cancer Research, Toronto, ON Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
| | - Michael D. Wilson
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
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22
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Palierne G, Fabre A, Solinhac R, Le Péron C, Avner S, Lenfant F, Fontaine C, Salbert G, Flouriot G, Arnal JF, Métivier R. Changes in Gene Expression and Estrogen Receptor Cistrome in Mouse Liver Upon Acute E2 Treatment. Mol Endocrinol 2016; 30:709-32. [PMID: 27164166 DOI: 10.1210/me.2015-1311] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transcriptional regulation by the estrogen receptor-α (ER) has been investigated mainly in breast cancer cell lines, but estrogens such as 17β-estradiol (E2) exert numerous extrareproductive effects, particularly in the liver, where E2 exhibits both protective metabolic and deleterious thrombotic actions. To analyze the direct and early transcriptional effects of estrogens in the liver, we determined the E2-sensitive transcriptome and ER cistrome in mice after acute administration of E2 or placebo. These analyses revealed the early induction of genes involved in lipid metabolism, which fits with the crucial role of ER in the prevention of liver steatosis. Characterization of the chromatin state of ER binding sites (BSs) in mice expressing or not ER demonstrated that ER is not required per se for the establishment and/or maintenance of chromatin modifications at the majority of its BSs. This is presumably a consequence of a strong overlap between ER and hepatocyte nuclear factor 4α BSs. In contrast, 40% of the BSs of the pioneer factor forkhead box protein a (Foxa2) were dependent upon ER expression, and ER expression also affected the distribution of nucleosomes harboring dimethylated lysine 4 of Histone H3 around Foxa2 BSs. We finally show that, in addition to a network of liver-specific transcription factors including CCAAT/enhancer-binding protein and hepatocyte nuclear factor 4α, ER might be required for proper Foxa2 function in this tissue.
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Affiliation(s)
- Gaëlle Palierne
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Aurélie Fabre
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Romain Solinhac
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Christine Le Péron
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Stéphane Avner
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Françoise Lenfant
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Coralie Fontaine
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Gilles Salbert
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Gilles Flouriot
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Jean-François Arnal
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
| | - Raphaël Métivier
- Equipe Spatio-Temporal Regulation of Transcription in Eukaryotes (SP@RTE) (G.P., C.L.P., S.A., G.S., R.M.), Unité Mixte de Recherche 6290 Centre National de la Recherche Scientifique (Institut de Genétique et Développement de Rennes), Université de Rennes 1, Campus de Beaulieu, and Equipe Transcription, Environment and Cancer (TREC) (G.F.), Inserm U1085-Institut de Recherche en Santé, Environnement et Travail, Rennes 35042 Cedex, France; and Equipe 9 "Estrogen Receptor: In Vivo Dissection and Modulation" (A.F., R.S., F.L., C.F., J.-F.A.), Inserm Unité 1048 (Institut des Maladies Métaboliques et Cardiovasculaires), Toulouse 31432 Cedex 4, France
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Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, Lee D, Kaestner KH, Zaret KS. The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Mol Cell 2016; 62:79-91. [PMID: 27058788 PMCID: PMC4826471 DOI: 10.1016/j.molcel.2016.03.001] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 02/05/2016] [Accepted: 02/29/2016] [Indexed: 12/20/2022]
Abstract
Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucleosomes and initiate gene regulatory events, often leading to the local opening of chromatin. However, the nucleosomal configuration of open chromatin and the basis for its regulation is unclear. We combined low and high levels of micrococcal nuclease (MNase) digestion along with core histone mapping to assess the nucleosomal configuration at enhancers and promoters in mouse liver. We find that MNase-accessible nucleosomes, bound by transcription factors, are retained more at liver-specific enhancers than at promoters and ubiquitous enhancers. The pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and allowing other liver-specific transcription factors to bind and stimulate transcription. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.
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Affiliation(s)
- Makiko Iwafuchi-Doi
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Greg Donahue
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Akshay Kakumanu
- Department of Biochemistry and Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jason A Watts
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dolim Lee
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Kenneth S Zaret
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA.
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24
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Turinetto V, Giachino C. Histone variants as emerging regulators of embryonic stem cell identity. Epigenetics 2016; 10:563-73. [PMID: 26114724 DOI: 10.1080/15592294.2015.1053682] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Dynamic regulation of chromatin structure is an important mechanism for balancing the pluripotency and cell fate decision in embryonic stem cells (ESCs). Indeed ESCs are characterized by unusual chromatin packaging, and a wide variety of chromatin regulators have been implicated in control of pluripotency and differentiation. Genome-wide maps of epigenetic factors have revealed a unique epigenetic signature in pluripotent ESCs and have contributed models to explain their plasticity. In addition to the well known epigenetic regulation through DNA methylation, histone posttranslational modifications, chromatin remodeling, and non-coding RNA, histone variants are emerging as important regulators of ESC identity. In this review, we summarize and discuss the recent progress that has highlighted the central role of histone variants in ESC pluripotency and ESC fate, focusing, in particular, on H1 variants, H2A variants H2A.X, H2A.Z and macroH2A and H3 variant H3.3.
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Affiliation(s)
- Valentina Turinetto
- a Department of Clinical and Biological Sciences; University of Turin ; Orbassano , Turin , Italy
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25
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Zhang G, Zhao Y, Liu Y, Kao LP, Wang X, Skerry B, Li Z. FOXA1 defines cancer cell specificity. SCIENCE ADVANCES 2016; 2:e1501473. [PMID: 27034986 PMCID: PMC4803482 DOI: 10.1126/sciadv.1501473] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
A transcription factor functions differentially and/or identically in multiple cell types. However, the mechanism for cell-specific regulation of a transcription factor remains to be elucidated. We address how a single transcription factor, forkhead box protein A1 (FOXA1), forms cell-specific genomic signatures and differentially regulates gene expression in four human cancer cell lines (HepG2, LNCaP, MCF7, and T47D). FOXA1 is a pioneer transcription factor in organogenesis and cancer progression. Genomewide mapping of FOXA1 by chromatin immunoprecipitation sequencing annotates that target genes associated with FOXA1 binding are mostly common to these cancer cells. However, most of the functional FOXA1 target genes are specific to each cancer cell type. Further investigations using CRISPR-Cas9 genome editing technology indicate that cell-specific FOXA1 regulation is attributable to unique FOXA1 binding, genetic variations, and/or potential epigenetic regulation. Thus, FOXA1 controls the specificity of cancer cell types. We raise a "flower-blooming" hypothesis for cell-specific transcriptional regulation based on these observations.
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26
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Deniz Ö, Flores O, Aldea M, Soler-López M, Orozco M. Nucleosome architecture throughout the cell cycle. Sci Rep 2016; 6:19729. [PMID: 26818620 PMCID: PMC4730144 DOI: 10.1038/srep19729] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/29/2015] [Indexed: 11/09/2022] Open
Abstract
Nucleosomes provide additional regulatory mechanisms to transcription and DNA replication by mediating the access of proteins to DNA. During the cell cycle chromatin undergoes several conformational changes, however the functional significance of these changes to cellular processes are largely unexplored. Here, we present the first comprehensive genome-wide study of nucleosome plasticity at single base-pair resolution along the cell cycle in Saccharomyces cerevisiae. We determined nucleosome organization with a specific focus on two regulatory regions: transcription start sites (TSSs) and replication origins (ORIs). During the cell cycle, nucleosomes around TSSs display rearrangements in a cyclic manner. In contrast to gap (G1 and G2) phases, nucleosomes have a fuzzier organization during S and M phases, Moreover, the choreography of nucleosome rearrangements correlate with changes in gene expression during the cell cycle, indicating a strong association between nucleosomes and cell cycle-dependent gene functionality. On the other hand, nucleosomes are more dynamic around ORIs along the cell cycle, albeit with tighter regulation in early firing origins, implying the functional role of nucleosomes on replication origins. Our study provides a dynamic picture of nucleosome organization throughout the cell cycle and highlights the subsequent impact on transcription and replication activity.
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Affiliation(s)
- Özgen Deniz
- Institute for Research in Biomedicine (IRB Barcelona). Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Joint BSC-CRG-IRB Program in Computational Biology. Baldiri Reixac 10-12. 08028 Barcelona, Spain
| | - Oscar Flores
- Institute for Research in Biomedicine (IRB Barcelona). Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Joint BSC-CRG-IRB Program in Computational Biology. Baldiri Reixac 10-12. 08028 Barcelona, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB) CSIC. Baldiri Reixac 4. 08028 Barcelona, Spain
| | - Montserrat Soler-López
- Institute for Research in Biomedicine (IRB Barcelona). Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Joint BSC-CRG-IRB Program in Computational Biology. Baldiri Reixac 10-12. 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Joint BSC-CRG-IRB Program in Computational Biology. Baldiri Reixac 10-12. 08028 Barcelona, Spain.,Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain
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27
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Pioneer transcription factors, chromatin dynamics, and cell fate control. Curr Opin Genet Dev 2016; 37:76-81. [PMID: 26826681 DOI: 10.1016/j.gde.2015.12.003] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/15/2015] [Accepted: 12/19/2015] [Indexed: 11/21/2022]
Abstract
Among the diverse transcription factors that are necessary to elicit changes in cell fate, both in embryonic development and in cellular reprogramming, a subset of factors are capable of binding to their target sequences on nucleosomal DNA and initiating regulatory events in silent chromatin. Such 'pioneer transcription factors' initiate cooperative interactions with other regulatory proteins to elicit changes in local chromatin structure. As a consequence of pioneer factor binding, the local chromatin can either become open and competent for activation, closed and repressed, or transcriptionally active. Understanding how pioneer factors initiate chromatin dynamics and how such can be blocked at heterochromatic sites provides insights into controlling cell fate transitions at will.
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Zaret KS. From Endoderm to Liver Bud: Paradigms of Cell Type Specification and Tissue Morphogenesis. Curr Top Dev Biol 2016; 117:647-69. [PMID: 26970006 DOI: 10.1016/bs.ctdb.2015.12.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The early specification, rapid growth and morphogenesis, and conserved functions of the embryonic liver across diverse model organisms have made the system an experimentally facile paradigm for understanding basic regulatory mechanisms that govern cell differentiation and organogenesis. This essay highlights concepts that have emerged from studies of the discrete steps of foregut endoderm development into the liver bud, as well as from modeling the steps via embryonic stem cell differentiation. Such concepts include understanding the chromatin basis for the competence of progenitor cells to develop into specific lineages; the importance of combinatorial signaling from different sources to induce cell fates; the impact of inductive signaling on preexisting chromatin states; the ability of separately specified domains of cells to merge into a common tissue; and the marked cell biological dynamics, including interactions with the developing vasculature, which establish the initial morphogenesis and patterning of a tissue. The principles gleaned from these studies, focusing on the 2 days it takes for the endoderm to develop into a liver bud, should be instructive for many other organogenic systems and for manipulating tissues in regenerative contexts for biomedical purposes.
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Affiliation(s)
- Kenneth S Zaret
- Institute for Regenerative Medicine, Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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29
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Ackermann AM, Wang Z, Schug J, Naji A, Kaestner KH. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Mol Metab 2016; 5:233-244. [PMID: 26977395 PMCID: PMC4770267 DOI: 10.1016/j.molmet.2016.01.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 12/30/2015] [Accepted: 01/03/2016] [Indexed: 01/20/2023] Open
Abstract
Objective Although glucagon-secreting α-cells and insulin-secreting β-cells have opposing functions in regulating plasma glucose levels, the two cell types share a common developmental origin and exhibit overlapping transcriptomes and epigenomes. Notably, destruction of β-cells can stimulate repopulation via transdifferentiation of α-cells, at least in mice, suggesting plasticity between these cell fates. Furthermore, dysfunction of both α- and β-cells contributes to the pathophysiology of type 1 and type 2 diabetes, and β-cell de-differentiation has been proposed to contribute to type 2 diabetes. Our objective was to delineate the molecular properties that maintain islet cell type specification yet allow for cellular plasticity. We hypothesized that correlating cell type-specific transcriptomes with an atlas of open chromatin will identify novel genes and transcriptional regulatory elements such as enhancers involved in α- and β-cell specification and plasticity. Methods We sorted human α- and β-cells and performed the “Assay for Transposase-Accessible Chromatin with high throughput sequencing” (ATAC-seq) and mRNA-seq, followed by integrative analysis to identify cell type-selective gene regulatory regions. Results We identified numerous transcripts with either α-cell- or β-cell-selective expression and discovered the cell type-selective open chromatin regions that correlate with these gene activation patterns. We confirmed cell type-selective expression on the protein level for two of the top hits from our screen. The “group specific protein” (GC; or vitamin D binding protein) was restricted to α-cells, while CHODL (chondrolectin) immunoreactivity was only present in β-cells. Furthermore, α-cell- and β-cell-selective ATAC-seq peaks were identified to overlap with known binding sites for islet transcription factors, as well as with single nucleotide polymorphisms (SNPs) previously identified as risk loci for type 2 diabetes. Conclusions We have determined the genetic landscape of human α- and β-cells based on chromatin accessibility and transcript levels, which allowed for detection of novel α- and β-cell signature genes not previously known to be expressed in islets. Using fine-mapping of open chromatin, we have identified thousands of potential cis-regulatory elements that operate in an endocrine cell type-specific fashion. Defined open chromatin regions in sorted human α- and β-cells using ATAC-seq. Detected type 2 diabetes-associated risk loci in human α- and β-cell open chromatin. Classified human α- and β-cell-specific transcripts using mRNA-seq. Discovered novel human α- and β-cell signature proteins. Identified potential gene regulatory regions by integrating ATAC- and mRNA-seq data.
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Key Words
- ARX, aristaless related homeobox
- ATAC-seq, Assay for Transposase-Accessible Chromatin with high throughput sequencing
- Alpha cell
- Beta cell
- CHODL, chondrolectin
- ChIP-seq, Chromatin Immunoprecipitation followed by high throughput sequencing
- DAPI, 4′,6-diamidino-2-phenylindole
- DPP4, dipeptidyl-peptidase 4
- Diabetes
- Epigenetics
- FACS, fluorescence-activated cell sorting
- FAIRE-seq, Formaldehyde-Assisted Isolation of Regulatory Elements followed by high throughput sequencing
- GC, group-specific protein
- GCG, glucagon
- GHRL, ghrelin
- IGF2, insulin like growth factor 2
- INS, insulin
- IRX2, iroquois homeobox 2
- Islet
- MAFA, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog A
- NEUROD1, neuronal differentiation 1
- Open chromatin
- PP, pancreatic polypeptide
- SNP, single nucleotide polymorphism
- SST, somatostatin
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Affiliation(s)
- Amanda M Ackermann
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA; Institute of Diabetes, Obesity, and Metabolism, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA.
| | - Zhiping Wang
- Institute for Biomedical Informatics, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA.
| | - Jonathan Schug
- Institute of Diabetes, Obesity, and Metabolism, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA; Department of Genetics, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA.
| | - Ali Naji
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA.
| | - Klaus H Kaestner
- Institute of Diabetes, Obesity, and Metabolism, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA; Department of Genetics, The University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia 19104, PA, USA.
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30
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Cauchy P, Maqbool MA, Zacarias-Cabeza J, Vanhille L, Koch F, Fenouil R, Gut M, Gut I, Santana MA, Griffon A, Imbert J, Moraes-Cabé C, Bories JC, Ferrier P, Spicuglia S, Andrau JC. Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation. Nucleic Acids Res 2015; 44:3567-85. [PMID: 26673693 PMCID: PMC4856961 DOI: 10.1093/nar/gkv1475] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/03/2015] [Indexed: 12/20/2022] Open
Abstract
Ets1 is a sequence-specific transcription factor that plays an important role during hematopoiesis, and is essential for the transition of CD4−/CD8− double negative (DN) to CD4+/CD8+ double positive (DP) thymocytes. Using genome-wide and functional approaches, we investigated the binding properties, transcriptional role and chromatin environment of Ets1 during this transition. We found that while Ets1 binding at distal sites was associated with active genes at both DN and DP stages, its enhancer activity was attained at the DP stage, as reflected by levels of the core transcriptional hallmarks H3K4me1/3, RNA Polymerase II and eRNA. This dual, stage-specific ability reflected a switch from non-T hematopoietic toward T-cell specific gene expression programs during the DN-to-DP transition, as indicated by transcriptome analyses of Ets1−/− thymic cells. Coincidentally, Ets1 associates more specifically with Runx1 in DN and with TCF1 in DP cells. We also provide evidence that Ets1 predominantly binds distal nucleosome-occupied regions in DN and nucleosome-depleted regions in DP. Finally and importantly, we demonstrate that Ets1 induces chromatin remodeling by displacing H3K4me1-marked nucleosomes. Our results thus provide an original model whereby the ability of a transcription factor to bind nucleosomal DNA changes during differentiation with consequences on its cognate enhancer activity.
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Affiliation(s)
- Pierre Cauchy
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Muhammad A Maqbool
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919 Route de Mende, Montpellier F-34293, France
| | - Joaquin Zacarias-Cabeza
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Laurent Vanhille
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Frederic Koch
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Romain Fenouil
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Marta Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac 4, Barcelona ES-08028, Spain
| | - Ivo Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac 4, Barcelona ES-08028, Spain
| | - Maria A Santana
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Aurélien Griffon
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Jean Imbert
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Carolina Moraes-Cabé
- INSERM UMR 1126 Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris F-75475, France
| | - Jean-Christophe Bories
- INSERM UMR 1126 Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris F-75475, France
| | - Pierre Ferrier
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Salvatore Spicuglia
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919 Route de Mende, Montpellier F-34293, France
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Mancini EJ, West MJ. How to Be a Pioneer: A One-Sided View. Trends Biochem Sci 2015; 40:547-548. [DOI: 10.1016/j.tibs.2015.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
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Yazdi PG, Pedersen BA, Taylor JF, Khattab OS, Chen YH, Chen Y, Jacobsen SE, Wang PH. Nucleosome Organization in Human Embryonic Stem Cells. PLoS One 2015; 10:e0136314. [PMID: 26305225 PMCID: PMC4549264 DOI: 10.1371/journal.pone.0136314] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/02/2015] [Indexed: 12/18/2022] Open
Abstract
The fundamental repeating unit of eukaryotic chromatin is the nucleosome. Besides being involved in packaging DNA, nucleosome organization plays an important role in transcriptional regulation and cellular identity. Currently, there is much debate about the major determinants of the nucleosome architecture of a genome and its significance with little being known about its role in stem cells. To address these questions, we performed ultra-deep sequencing of nucleosomal DNA in two human embryonic stem cell lines and integrated our data with numerous epigenomic maps. Our analyses have revealed that the genome is a determinant of nucleosome organization with transcriptionally inactive regions characterized by a “ground state” of nucleosome profiles driven by underlying DNA sequences. DNA sequence preferences are associated with heterogeneous chromatin organization around transcription start sites. Transcription, histone modifications, and DNA methylation alter this “ground state” by having distinct effects on both nucleosome positioning and occupancy. As the transcriptional rate increases, nucleosomes become better positioned. Exons transcribed and included in the final spliced mRNA have distinct nucleosome profiles in comparison to exons not included at exon-exon junctions. Genes marked by the active modification H3K4m3 are characterized by lower nucleosome occupancy before the transcription start site compared to genes marked by the inactive modification H3K27m3, while bivalent domains, genes associated with both marks, lie exactly in the middle. Combinatorial patterns of epigenetic marks (chromatin states) are associated with unique nucleosome profiles. Nucleosome organization varies around transcription factor binding in enhancers versus promoters. DNA methylation is associated with increasing nucleosome occupancy and different types of methylations have distinct location preferences within the nucleosome core particle. Finally, computational analysis of nucleosome organization alone is sufficient to elucidate much of the circuitry of pluripotency. Our results, suggest that nucleosome organization is associated with numerous genomic and epigenomic processes and can be used to elucidate cellular identity.
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Affiliation(s)
- Puya G. Yazdi
- UC Irvine Diabetes Center, University of California Irvine, Irvine, California, United States of America
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, California, United States of America
- Department of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Brian A. Pedersen
- UC Irvine Diabetes Center, University of California Irvine, Irvine, California, United States of America
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, California, United States of America
- Department of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Jared F. Taylor
- UC Irvine Diabetes Center, University of California Irvine, Irvine, California, United States of America
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, California, United States of America
- Department of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Omar S. Khattab
- UC Irvine Diabetes Center, University of California Irvine, Irvine, California, United States of America
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, California, United States of America
| | - Yu-Han Chen
- UC Irvine Diabetes Center, University of California Irvine, Irvine, California, United States of America
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, California, United States of America
- Department of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Yumay Chen
- UC Irvine Diabetes Center, University of California Irvine, Irvine, California, United States of America
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, California, United States of America
- Department of Medicine, University of California Irvine, Irvine, California, United States of America
| | - Steven E. Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ping H. Wang
- UC Irvine Diabetes Center, University of California Irvine, Irvine, California, United States of America
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, California, United States of America
- Department of Medicine, University of California Irvine, Irvine, California, United States of America
- Department of Biological Chemistry, University of California Irvine, Irvine, California, United States of America
- Department of Physiology & Biophysics, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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33
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Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell 2015; 161:555-568. [PMID: 25892221 DOI: 10.1016/j.cell.2015.03.017] [Citation(s) in RCA: 528] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/24/2014] [Accepted: 02/15/2015] [Indexed: 12/23/2022]
Abstract
Pioneer transcription factors (TFs) access silent chromatin and initiate cell-fate changes, using diverse types of DNA binding domains (DBDs). FoxA, the paradigm pioneer TF, has a winged helix DBD that resembles linker histone and thereby binds its target sites on nucleosomes and in compacted chromatin. Herein, we compare the nucleosome and chromatin targeting activities of Oct4 (POU DBD), Sox2 (HMG box DBD), Klf4 (zinc finger DBD), and c-Myc (bHLH DBD), which together reprogram somatic cells to pluripotency. Purified Oct4, Sox2, and Klf4 proteins can bind nucleosomes in vitro, and in vivo they preferentially target silent sites enriched for nucleosomes. Pioneer activity relates simply to the ability of a given DBD to target partial motifs displayed on the nucleosome surface. Such partial motif recognition can occur by coordinate binding between factors. Our findings provide insight into how pioneer factors can target naive chromatin sites.
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Henagan TM, Stefanska B, Fang Z, Navard AM, Ye J, Lenard NR, Devarshi PP. Sodium butyrate epigenetically modulates high-fat diet-induced skeletal muscle mitochondrial adaptation, obesity and insulin resistance through nucleosome positioning. Br J Pharmacol 2015; 172:2782-98. [PMID: 25559882 DOI: 10.1111/bph.13058] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/24/2014] [Accepted: 12/15/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND PURPOSE Sodium butyrate (NaB), an epigenetic modifier, is effective in promoting insulin sensitivity. The specific genomic loci and mechanisms underlying epigenetically induced obesity and insulin resistance and the targets of NaB are not fully understood. EXPERIMENTAL APPROACH The anti-diabetic and anti-obesity effects of NaB treatment were measured by comparing phenotypes and physiologies of C57BL/6J mice fed a low-fat diet (LF), high-fat diet (HF) or high-fat diet plus NaB (HF + NaB) for 10 weeks. We determined a possible mechanism of NaB action through induction of beneficial skeletal muscle mitochondrial adaptations and applied microccocal nuclease digestion with sequencing (MNase-seq) to assess whole genome differences in nucleosome occupancy or positioning and to identify associated epigenetic targets of NaB. KEY RESULTS NaB prevented HF diet-induced increases in body weight and adiposity without altering food intake or energy expenditure, improved insulin sensitivity as measured by glucose and insulin tolerance tests, and decreased respiratory exchange ratio. In skeletal muscle, NaB increased the percentage of type 1 fibres, improved acylcarnitine profiles as measured by metabolomics and produced a chromatin structure, determined by MNase-seq, similar to that seen in LF. Targeted analysis of representative nuclear-encoded mitochondrial genes showed specific repositioning of the -1 nucleosome in association with altered gene expression. CONCLUSIONS AND IMPLICATIONS NaB treatment may be an effective pharmacological approach for type 2 diabetes and obesity by inducing -1 nucleosome repositioning within nuclear-encoded mitochondrial genes, causing skeletal muscle mitochondrial adaptations that result in more complete β-oxidation and a lean, insulin sensitive phenotype.
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Affiliation(s)
- Tara M Henagan
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Barbara Stefanska
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Zhide Fang
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Alexandra M Navard
- Neurosignaling Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Jianping Ye
- Antioxidant and Gene Regulation Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Natalie R Lenard
- Department of Sciences, Our Lady of the Lake College, Baton Rouge, LA, USA
| | - Prasad P Devarshi
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
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35
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Taher L, Narlikar L, Ovcharenko I. Identification and computational analysis of gene regulatory elements. Cold Spring Harb Protoc 2015; 2015:pdb.top083642. [PMID: 25561628 PMCID: PMC5885252 DOI: 10.1101/pdb.top083642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the last two decades, advances in experimental and computational technologies have greatly facilitated genomic research. Next-generation sequencing technologies have made de novo sequencing of large genomes affordable, and powerful computational approaches have enabled accurate annotations of genomic DNA sequences. Charting functional regions in genomes must account for not only the coding sequences, but also noncoding RNAs, repetitive elements, chromatin states, epigenetic modifications, and gene regulatory elements. A mix of comparative genomics, high-throughput biological experiments, and machine learning approaches has played a major role in this truly global effort. Here we describe some of these approaches and provide an account of our current understanding of the complex landscape of the human genome. We also present overviews of different publicly available, large-scale experimental data sets and computational tools, which we hope will prove beneficial for researchers working with large and complex genomes.
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Affiliation(s)
- Leila Taher
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, 18051 Rostock, Germany
| | - Leelavati Narlikar
- Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
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36
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PGC1α -1 Nucleosome Position and Splice Variant Expression and Cardiovascular Disease Risk in Overweight and Obese Individuals. PPAR Res 2014; 2014:895734. [PMID: 25614734 PMCID: PMC4295622 DOI: 10.1155/2014/895734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/26/2014] [Indexed: 11/17/2022] Open
Abstract
PGC1α, a transcriptional coactivator, interacts with PPARs and others to regulate skeletal muscle metabolism. PGC1α undergoes splicing to produce several mRNA variants, with the NTPGC1α variant having a similar biological function to the full length PGC1α (FLPGC1α). CVD is associated with obesity and T2D and a lower percentage of type 1 oxidative fibers and impaired mitochondrial function in skeletal muscle, characteristics determined by PGC1α expression. PGC1α expression is epigenetically regulated in skeletal muscle to determine mitochondrial adaptations, and epigenetic modifications may regulate mRNA splicing. We report in this paper that skeletal muscle PGC1α -1 nucleosome (-1N) position is associated with splice variant NTPGC1α but not FLPGC1α expression. Division of participants based on the -1N position revealed that those individuals with a -1N phased further upstream from the transcriptional start site (UP) expressed lower levels of NTPGC1α than those with the -1N more proximal to TSS (DN). UP showed an increase in body fat percentage and serum total and LDL cholesterol. These findings suggest that the -1N may be a potential epigenetic regulator of NTPGC1α splice variant expression, and -1N position and NTPGC1α variant expression in skeletal muscle are linked to CVD risk. This trial is registered with clinicaltrials.gov, identifier NCT00458133.
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37
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Liu H, Jin T, Guan J, Zhou S. Histone modifications involved in cassette exon inclusions: a quantitative and interpretable analysis. BMC Genomics 2014; 15:1148. [PMID: 25526687 PMCID: PMC4378014 DOI: 10.1186/1471-2164-15-1148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/20/2014] [Indexed: 11/16/2022] Open
Abstract
Background Chromatin structure and epigenetic modifications have been shown to involve in the co-transcriptional splicing of RNA precursors. In particular, some studies have suggested that some types of histone modifications (HMs) may participate in the alternative splicing and function as exon marks. However, most existing studies pay attention to the qualitative relationship between epigenetic modifications and exon inclusion. The quantitative analysis that reveals to what extent each type of epigenetic modification is responsible for exon inclusion is very helpful for us to understand the splicing process. Results In this paper, we focus on the quantitative analysis of HMs’ influence on the inclusion of cassette exons (CEs) into mature RNAs. With the high-throughput ChIP-seq and RNA-seq data obtained from ENCODE website, we modeled the association of HMs with CE inclusions by logistic regression whose coefficients are meaningful and interpretable for us to reveal the effect of each type of HM. Three type of HMs, H3K36me3, H3K9me3 and H4K20me1, were found to play major role in CE inclusions. HMs’ effect on CE inclusions is conservative across cell types, and does not depend on the expression levels of the genes hosting CEs. HMs located in the flanking regions of CEs were also taken into account in our analysis, and HMs within bounded flanking regions were shown to affect moderately CE inclusions. Moreover, we also found that HMs on CEs whose length is approximately close to nucleosomal-DNA length affect greatly on CE inclusion. Conclusions We suggested that a few types of HMs correlate closely to alternative splicing and perhaps function jointly with splicing machinery to regulate the inclusion level of exons. Our findings are helpful to understand HMs’ effect on exon definition, as well as the mechanism of co-transcriptional splicing. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1148) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Shuigeng Zhou
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 200433 Shanghai, China.
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38
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Beck S, Lee BK, Rhee C, Song J, Woo AJ, Kim J. CpG island-mediated global gene regulatory modes in mouse embryonic stem cells. Nat Commun 2014; 5:5490. [PMID: 25405324 PMCID: PMC4236720 DOI: 10.1038/ncomms6490] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 10/03/2014] [Indexed: 12/13/2022] Open
Abstract
Both transcriptional and epigenetic regulations are fundamental for the control of eukaryotic gene expression. Here we perform a compendium analysis of >200 large sequencing data sets to elucidate the regulatory logic of global gene expression programs in mouse embryonic stem (ES) cells. We define four major classes of DNA-binding proteins (Core, PRC, MYC and CTCF) based on their target co-occupancy, and discover reciprocal regulation between the MYC and PRC classes for the activity of nearly all genes under the control of the CpG island (CGI)-containing promoters. This CGI-dependent regulatory mode explains the functional segregation between CGI-containing and CGI-less genes during early development. By defining active enhancers based on the co-occupancy of the Core class, we further demonstrate their additive roles in CGI-containing gene expression and cell type-specific roles in CGI-less gene expression. Altogether, our analyses provide novel insights into previously unknown CGI-dependent global gene regulatory modes.
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Affiliation(s)
- Samuel Beck
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-Kyu Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Catherine Rhee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jawon Song
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, Texas 78758, USA
| | - Andrew J Woo
- School of Medicine and Pharmacology, Royal Perth Hospital Unit, The University of Western Australia, Perth, WA 6000, Australia
| | - Jonghwan Kim
- 1] Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA [2] Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA [3] Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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39
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Bochkis IM, Przybylski D, Chen J, Regev A. Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver. Cell Rep 2014; 9:996-1006. [PMID: 25437555 PMCID: PMC4250828 DOI: 10.1016/j.celrep.2014.09.048] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/15/2014] [Accepted: 09/24/2014] [Indexed: 12/27/2022] Open
Abstract
Aging is accompanied by physiological impairments, which, in insulin-responsive tissues, including the liver, predispose individuals to metabolic disease. However, the molecular mechanisms underlying these changes remain largely unknown. Here, we analyze genome-wide profiles of RNA and chromatin organization in the liver of young (3 months) and old (21 months) mice. Transcriptional changes suggest that derepression of the nuclear receptors PPARα, PPARγ, and LXRα in aged mouse liver leads to activation of targets regulating lipid synthesis and storage, whereas age-dependent changes in nucleosome occupancy are associated with binding sites for both known regulators (forkhead factors and nuclear receptors) and candidates associated with nuclear lamina (Hdac3 and Srf) implicated to govern metabolic function of aging liver. Winged-helix transcription factor Foxa2 and nuclear receptor corepressor Hdac3 exhibit a reciprocal binding pattern at PPARα targets contributing to gene expression changes that lead to steatosis in aged liver.
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Affiliation(s)
- Irina M Bochkis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | | | - Jenny Chen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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40
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West JA, Cook A, Alver BH, Stadtfeld M, Deaton AM, Hochedlinger K, Park PJ, Tolstorukov MY, Kingston RE. Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming. Nat Commun 2014; 5:4719. [PMID: 25158628 PMCID: PMC4217530 DOI: 10.1038/ncomms5719] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 07/16/2014] [Indexed: 01/23/2023] Open
Abstract
Chromatin structure determines DNA accessibility. We compare nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs) and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach to identify regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. Surprisingly, most chromatin remains unchanged; a majority of rearrangements appear to affect a single nucleosome. RoDs are enriched at genes and regulatory elements, including enhancers associated with pluripotency and differentiation. RoDs co-localize with binding sites of key developmental regulators, including the reprogramming factors Klf4, Oct4/Sox2 and c-Myc. Nucleosomal landscapes in ESC enhancers are extensively altered, exhibiting lower nucleosome occupancy in pluripotent cells than in somatic cells. Most changes are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of cell differentiation and reprogramming and likely identify regulatory regions essential for these processes. Changes in chromatin structure impact gene expression programs by modulating accessibility to the transcription machinery. Here, West et al. explore differences in nucleosome occupancy between mammalian pluripotent and somatic cells and uncover regulatory regions likely to play key roles in determining cell identity.
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Affiliation(s)
- Jason A West
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] [4]
| | - April Cook
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3]
| | - Burak H Alver
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthias Stadtfeld
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, The Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
| | - Aimee M Deaton
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Konrad Hochedlinger
- 1] Howard Hughes Medical Institute and the Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] The Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Peter J Park
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Y Tolstorukov
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2]
| | - Robert E Kingston
- 1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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41
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Drouin J. Minireview: pioneer transcription factors in cell fate specification. Mol Endocrinol 2014; 28:989-98. [PMID: 24825399 DOI: 10.1210/me.2014-1084] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The specification of cell fate is critical for proper cell differentiation and organogenesis. In endocrine tissues, this process leads to the differentiation, often a multistep process, of hormone-producing cells. This process is driven by a combination of transcription factors (TFs) that includes general factor, tissue-restricted, and/or cell-restricted factors. The last 2 decades have seen the discovery of many TFs of restricted expression and function in endocrine tissues. These factors are typically critical for expression of hormone-coding genes as well as for differentiation and proper function of hormone-producing cells. Further, genes encoding these tissue-restricted TFs are themselves subject to mutations that cause hormone deficiencies. Although the model that emerged from these 2 decades is one in which a specific combination of TFs drives a unique cell specification and genetic program, recent findings have led to the discovery of TFs that have the unique property of being able to remodel chromatin and thus modify the epigenome. Most importantly, such factors, known as pioneer TFs, appear to play critical roles in programming the epigenome during the successive steps involved in cell specification. This review summarizes our current understanding of the mechanisms for pioneer TF remodeling of chromatin. Currently, very few TFs that have proven pioneer activity are known, but it will be critical to identify these factors and understand their mechanisms of action if we are to harness the potential of regenerative therapies in endocrinology.
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Affiliation(s)
- Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montréal, Quebec, H2W 1R7 Canada
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42
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Abstract
Robustness, the maintenance of a character in the presence of genetic change, can help preserve adaptive traits but also may hinder evolvability, the ability to bring forth novel adaptations. We used genotype networks to analyze the binding site repertoires of 193 transcription factors from mice and yeast, providing empirical evidence that robustness and evolvability need not be conflicting properties. Network vertices represent binding sites where two sites are connected if they differ in a single nucleotide. We show that the binding sites of larger genotype networks are not only more robust, but the sequences adjacent to such networks can also bind more transcription factors, thus demonstrating that robustness can facilitate evolvability.
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Affiliation(s)
- Joshua L Payne
- University of Zurich, Institute of Evolutionary Biology and Environmental Studies, Zurich, Switzerland
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43
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Sherwood RI, Hashimoto T, O'Donnell CW, Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T, Gifford DK. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol 2014; 32:171-178. [PMID: 24441470 PMCID: PMC3951735 DOI: 10.1038/nbt.2798] [Citation(s) in RCA: 312] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 12/16/2013] [Indexed: 11/12/2022]
Abstract
We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase I hypersensitivity analysis followed by sequencing (DNase-seq) experiment with accuracy comparable to that of chromatin immunoprecipitation followed by sequencing (ChIP-seq). We applied PIQ to analyze DNase-seq data from mouse embryonic stem cells differentiating into prepancreatic and intestinal endoderm. We identified 120 and experimentally validated eight 'pioneer' TF families that dynamically open chromatin. Four pioneer TF families only opened chromatin in one direction from their motifs. Furthermore, we identified 'settler' TFs whose genomic binding is principally governed by proximity to open chromatin. Our results support a model of hierarchical TF binding in which directional and nondirectional pioneer activity shapes the chromatin landscape for population by settler TFs.
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Affiliation(s)
- Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Tatsunori Hashimoto
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Charles W O'Donnell
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, 7 Divinity Avenue, Cambridge, MA 02138
| | - Sophia Lewis
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Amira A Barkal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - John Peter van Hoff
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Vivek Karun
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Tommi Jaakkola
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, 7 Divinity Avenue, Cambridge, MA 02138
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Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS. Canonical nucleosome organization at promoters forms during genome activation. Genome Res 2013; 24:260-6. [PMID: 24285721 PMCID: PMC3912416 DOI: 10.1101/gr.157750.113] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of histone H3 lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.
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Affiliation(s)
- Yong Zhang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
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45
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Liu H, Zhang R, Xiong W, Guan J, Zhuang Z, Zhou S. A comparative evaluation on prediction methods of nucleosome positioning. Brief Bioinform 2013; 15:1014-27. [PMID: 24023366 DOI: 10.1093/bib/bbt062] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Nucleosome positioning plays an essential role in cellular processes by modulating accessibility of DNA to proteins. Many computational models have been developed to predict genome-wide nucleosome positions from DNA sequences. Comparative analysis of predicted and experimental nucleosome positioning maps facilitates understanding the regulatory mechanisms of transcription and DNA replication. Therefore, a comprehensive evaluation of existing computational methods is important and useful for biologists to choose appropriate ones in their research. In this article, we carried out a performance comparison among eight widely used computational methods on four species including yeast, fruitfly, mouse and human. In particular, we compared these methods on different regions of each species such as gene sequences, promoters and 5'UTR exons. The experimental results show that the performances of the two latest versions of the thermodynamic model are relatively steadier than the other four methods. Moreover, these methods are workable on four species, but their performances decrease gradually from yeast to human, indicating that the fundamental mechanism of nucleosome positioning is conserved through the evolution process, but more and more factors participate in the determination of nucleosome positions, which leads to sophisticated regulation mechanisms.
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46
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Genome-wide analysis of chromatin states reveals distinct mechanisms of sex-dependent gene regulation in male and female mouse liver. Mol Cell Biol 2013; 33:3594-610. [PMID: 23836885 DOI: 10.1128/mcb.00280-13] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromatin state maps were developed to elucidate sex differences in chromatin structure and their impact on sex-differential chromatin accessibility and sex-biased gene expression in mouse liver. Genes in active, inactive, and poised chromatin states exhibited differential responsiveness to ligand-activated nuclear receptors and distinct enrichments for functional gene categories. Sex-biased genes were clustered by chromatin environments and mapped to DNase-hypersensitive sites (DHS) classified by sex bias in chromatin accessibility and enhancer modifications. Results were integrated with genome-wide binding data for five transcription factors implicated in growth hormone-regulated, sex-biased liver gene expression, leading to the following findings. (i) Sex-biased DHS, but not sex-biased genes, are frequently characterized by sex-differential chromatin states, indicating distal regulation. (ii) Trimethylation of histone H3 at K27 (H3K27me3) is a major sex-biased repressive mark at highly female-biased but not at highly male-biased genes. (iii) FOXA factors are associated with sex-dependent chromatin opening at male-biased but not female-biased regulatory sites. (iv) Sex-biased STAT5 binding is enriched at sex-biased DHS marked as active enhancers and preferentially targets sex-biased genes with sex-differences in local chromatin marks. (v) The male-biased repressor BCL6 preferentially targets female-biased genes and regulatory sites in a sex-independent chromatin state. (vi) CUX2, a female-specific repressor of male-biased genes, also activates strongly female-biased genes, in association with loss of H3K27me3 marks. Chromatin states are thus a major determinant of sex-biased chromatin accessibility and gene expression, with FOXA pioneer factors proposed to confer sex-dependent chromatin opening and STAT5, but not BCL6, regulating sex-biased genes by binding to sites in a sex-biased chromatin state.
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Erkek S, Hisano M, Liang CY, Gill M, Murr R, Dieker J, Schübeler D, van der Vlag J, Stadler MB, Peters AHFM. Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa. Nat Struct Mol Biol 2013; 20:868-75. [PMID: 23770822 DOI: 10.1038/nsmb.2599] [Citation(s) in RCA: 245] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/29/2013] [Indexed: 12/21/2022]
Abstract
In mammalian spermatozoa, most but not all of the genome is densely packaged by protamines. Here we reveal the molecular logic underlying the retention of nucleosomes in mouse spermatozoa, which contain only 1% residual histones. We observe high enrichment throughout the genome of nucleosomes at CpG-rich sequences that lack DNA methylation. Residual nucleosomes are largely composed of the histone H3.3 variant and are trimethylated at Lys4 of histone H3 (H3K4me3). Canonical H3.1 and H3.2 histones are also enriched at CpG-rich promoters marked by Polycomb-mediated H3K27me3, a modification predictive of gene repression in preimplantation embryos. Histone variant-specific nucleosome retention in sperm is strongly associated with nucleosome turnover in round spermatids. Our data show evolutionary conservation of the basic principles of nucleosome retention in mouse and human sperm, supporting a model of epigenetic inheritance by nucleosomes between generations.
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Affiliation(s)
- Serap Erkek
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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Grøntved L, John S, Baek S, Liu Y, Buckley JR, Vinson C, Aguilera G, Hager GL. C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements. EMBO J 2013; 32:1568-83. [PMID: 23665916 DOI: 10.1038/emboj.2013.106] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/10/2013] [Indexed: 01/22/2023] Open
Abstract
Mechanisms regulating transcription factor interaction with chromatin in intact mammalian tissues are poorly understood. Exploiting an adrenalectomized mouse model with depleted endogenous glucocorticoids, we monitor changes of the chromatin landscape in intact liver tissue following glucocorticoid injection. Upon activation of the glucocorticoid receptor (GR), proximal regions of activated and repressed genes are remodelled, and these remodelling events correlate with RNA polymerase II occupancy of regulated genes. GR is exclusively associated with accessible chromatin and 62% percent of GR-binding sites are occupied by C/EBPβ. At the majority of these sites, chromatin is preaccessible suggesting a priming function of C/EBPβ for GR recruitment. Disruption of C/EBPβ binding to chromatin results in attenuation of pre-programmed chromatin accessibility, GR recruitment and GR-induced chromatin remodelling specifically at sites co-occupied by GR and C/EBPβ. Collectively, we demonstrate a highly cooperative mechanism by which C/EBPβ regulates selective GR binding to the genome in liver tissue. We suggest that selective targeting of GR in other tissues is likely mediated by the combined action of cell-specific priming proteins and chromatin remodellers.
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Affiliation(s)
- Lars Grøntved
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Teif VB, Erdel F, Beshnova DA, Vainshtein Y, Mallm JP, Rippe K. Taking into account nucleosomes for predicting gene expression. Methods 2013; 62:26-38. [PMID: 23523656 DOI: 10.1016/j.ymeth.2013.03.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 03/10/2013] [Indexed: 01/10/2023] Open
Abstract
The eukaryotic genome is organized in a chain of nucleosomes that consist of 145-147 bp of DNA wrapped around a histone octamer protein core. Binding of transcription factors (TF) to nucleosomal DNA is frequently impeded, which makes it a challenging task to calculate TF occupancy at a given regulatory genomic site for predicting gene expression. Here, we review methods to calculate TF binding to DNA in the presence of nucleosomes. The main theoretical problems are (i) the computation speed that is becoming a bottleneck when partial unwrapping of DNA from the nucleosome is considered, (ii) the perturbation of the binding equilibrium by the activity of ATP-dependent chromatin remodelers, which translocate nucleosomes along the DNA, and (iii) the model parameterization from high-throughput sequencing data and fluorescence microscopy experiments in living cells. We discuss strategies that address these issues to efficiently compute transcription factor binding in chromatin.
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Affiliation(s)
- Vladimir B Teif
- Research Group Genome Organization & Function, Deutsches Krebsforschungszentrum-DKFZ & BioQuant, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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Tennant BR, Robertson AG, Kramer M, Li L, Zhang X, Beach M, Thiessen N, Chiu R, Mungall K, Whiting CJ, Sabatini PV, Kim A, Gottardo R, Marra MA, Lynn FC, Jones SJM, Hoodless PA, Hoffman BG. Identification and analysis of murine pancreatic islet enhancers. Diabetologia 2013; 56:542-52. [PMID: 23238790 PMCID: PMC4773896 DOI: 10.1007/s00125-012-2797-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/20/2012] [Indexed: 01/05/2023]
Abstract
AIMS/HYPOTHESIS The paucity of information on the epigenetic barriers that are blocking reprogramming protocols, and on what makes a beta cell unique, has hampered efforts to develop novel beta cell sources. Here, we aimed to identify enhancers in pancreatic islets, to understand their developmental ontologies, and to identify enhancers unique to islets to increase our understanding of islet-specific gene expression. METHODS We combined H3K4me1-based nucleosome predictions with pancreatic and duodenal homeobox 1 (PDX1), neurogenic differentiation 1 (NEUROD1), v-Maf musculoaponeurotic fibrosarcoma oncogene family, protein A (MAFA) and forkhead box A2 (FOXA2) occupancy data to identify enhancers in mouse islets. RESULTS We identified 22,223 putative enhancer loci in in vivo mouse islets. Our validation experiments suggest that nearly half of these loci are active in regulating islet gene expression, with the remaining regions probably poised for activity. We showed that these loci have at least nine developmental ontologies, and that islet enhancers predominately acquire H3K4me1 during differentiation. We next discriminated 1,799 enhancers unique to islets and showed that these islet-specific enhancers have reduced association with annotated genes, and identified a subset that are instead associated with novel islet-specific long non-coding RNAs (lncRNAs). CONCLUSIONS/INTERPRETATIONS Our results indicate that genes with islet-specific expression and function tend to have enhancers devoid of histone methylation marks or, less often, that are bivalent or repressed, in embryonic stem cells and liver. Further, we identify a subset of enhancers unique to islets that are associated with novel islet-specific genes and lncRNAs. We anticipate that these data will facilitate the development of novel sources of functional beta cell mass.
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Affiliation(s)
- B. R. Tennant
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - A. G. Robertson
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - M. Kramer
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - L. Li
- Biostatistics Branch, National Institute of Environmental Health Sciences/NIH, Research Triangle Park, NC, USA
| | - X. Zhang
- Department of Statistics, University of British Columbia, Vancouver, BC, Canada
| | - M. Beach
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - N. Thiessen
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - R. Chiu
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - K. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - C. J. Whiting
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - P. V. Sabatini
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - A. Kim
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
| | - R. Gottardo
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M. A. Marra
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - F. C. Lynn
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - S. J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - P. A. Hoodless
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - B. G. Hoffman
- Child and Family Research Institute, British Columbia Children’s Hospital and Sunny Hill Health Centre, Room A4-185, 950 W28th Avenue, Vancouver, BC, Canada V5Z 4H4
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
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