301
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Abstract
Three recent studies measure individual variation in regulatory DNA accessibility. What do they tell us about the prospects of assessing variation in single cells and across populations?
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Affiliation(s)
- Matthew T Maurano
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY 10016, USA; Department of Pathology, New York University Langone Medical Center, New York, NY 10016, USA
| | - John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA 98115, USA; Division of Oncology, Department of Medicine, University of Washington, Seattle, WA 98115, USA.
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302
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Zoller B, Nicolas D, Molina N, Naef F. Structure of silent transcription intervals and noise characteristics of mammalian genes. Mol Syst Biol 2015. [PMID: 26215071 PMCID: PMC4547851 DOI: 10.15252/msb.20156257] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mammalian transcription occurs stochastically in short bursts interspersed by silent intervals showing a refractory period. However, the underlying processes and consequences on fluctuations in gene products are poorly understood. Here, we use single allele time-lapse recordings in mouse cells to identify minimal models of promoter cycles, which inform on the number and durations of rate-limiting steps responsible for refractory periods. The structure of promoter cycles is gene specific and independent of genomic location. Typically, five rate-limiting steps underlie the silent periods of endogenous promoters, while minimal synthetic promoters exhibit only one. Strikingly, endogenous or synthetic promoters with TATA boxes show simplified two-state promoter cycles. Since transcriptional bursting constrains intrinsic noise depending on the number of promoter steps, this explains why TATA box genes display increased intrinsic noise genome-wide in mammals, as revealed by single-cell RNA-seq. These findings have implications for basic transcription biology and shed light on interpreting single-cell RNA-counting experiments.
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Affiliation(s)
- Benjamin Zoller
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Damien Nicolas
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nacho Molina
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Felix Naef
- The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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303
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Elucidating the mechanisms of transcription regulation during heart development by next-generation sequencing. J Hum Genet 2015. [PMID: 26202577 DOI: 10.1038/jhg.2015.84] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dysregulation of transcription is associated with the pathogenesis of cardiovascular diseases, including congenital heart diseases and heart failure. However, it remains unclear how transcription factors regulate transcription in the heart and which genes are associated with cardiovascular diseases in humans. Development of genome-wide analyses using next-generation sequencers provides powerful methods to determine how these transcription factors and chromatin regulators control gene expressions and to identify causative genes in cardiovascular diseases. These technologies have revealed that transcription during heart development is elaborately regulated by multiple cardiac transcription factors. In this review, we discuss the recent progress toward understanding the molecular mechanisms of how transcriptional dysregulation leads to cardiovascular diseases.
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304
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Abstract
Environmental agents are constantly challenging cells by damaging DNA, leading to the blockage of transcription elongation. How do cells deal with transcription-blockage and how is transcription restarted after the blocking lesions are removed? Here we review the processes responsible for the removal of transcription-blocking lesions, as well as mechanisms of transcription restart. We also discuss recent data suggesting that blocked RNA polymerases may not resume transcription from the site of the lesion following its removal but, rather, are forced to start over from the beginning of genes.
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305
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Dror I, Golan T, Levy C, Rohs R, Mandel-Gutfreund Y. A widespread role of the motif environment in transcription factor binding across diverse protein families. Genome Res 2015; 25:1268-80. [PMID: 26160164 PMCID: PMC4561487 DOI: 10.1101/gr.184671.114] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 07/08/2015] [Indexed: 12/12/2022]
Abstract
Transcriptional regulation requires the binding of transcription factors (TFs) to short sequence-specific DNA motifs, usually located at the gene regulatory regions. Interestingly, based on a vast amount of data accumulated from genomic assays, it has been shown that only a small fraction of all potential binding sites containing the consensus motif of a given TF actually bind the protein. Recent in vitro binding assays, which exclude the effects of the cellular environment, also demonstrate selective TF binding. An intriguing conjecture is that the surroundings of cognate binding sites have unique characteristics that distinguish them from other sequences containing a similar motif that are not bound by the TF. To test this hypothesis, we conducted a comprehensive analysis of the sequence and DNA shape features surrounding the core-binding sites of 239 and 56 TFs extracted from in vitro HT-SELEX binding assays and in vivo ChIP-seq data, respectively. Comparing the nucleotide content of the regions around the TF-bound sites to the counterpart unbound regions containing the same consensus motifs revealed significant differences that extend far beyond the core-binding site. Specifically, the environment of the bound motifs demonstrated unique sequence compositions, DNA shape features, and overall high similarity to the core-binding motif. Notably, the regions around the binding sites of TFs that belong to the same TF families exhibited similar features, with high agreement between the in vitro and in vivo data sets. We propose that these unique features assist in guiding TFs to their cognate binding sites.
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Affiliation(s)
- Iris Dror
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel; Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Tamar Golan
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carmit Levy
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Remo Rohs
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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306
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Deng T, Zhu ZI, Zhang S, Postnikov Y, Huang D, Horsch M, Furusawa T, Beckers J, Rozman J, Klingenspor M, Amarie O, Graw J, Rathkolb B, Wolf E, Adler T, Busch DH, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, van der Velde A, Tessarollo L, Ovcherenko I, Landsman D, Bustin M. Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers. Genome Res 2015; 25:1295-308. [PMID: 26156321 PMCID: PMC4561489 DOI: 10.1101/gr.192229.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/07/2015] [Indexed: 12/29/2022]
Abstract
DNase I hypersensitive sites (DHSs) are a hallmark of chromatin regions containing regulatory DNA such as enhancers and promoters; however, the factors affecting the establishment and maintenance of these sites are not fully understood. We now show that HMGN1 and HMGN2, nucleosome-binding proteins that are ubiquitously expressed in vertebrate cells, maintain the DHS landscape of mouse embryonic fibroblasts (MEFs) synergistically. Loss of one of these HMGN variants led to a compensatory increase of binding of the remaining variant. Genome-wide mapping of the DHSs in Hmgn1(-/-), Hmgn2(-/-), and Hmgn1(-/-)n2(-/-) MEFs reveals that loss of both, but not a single HMGN variant, leads to significant remodeling of the DHS landscape, especially at enhancer regions marked by H3K4me1 and H3K27ac. Loss of HMGN variants affects the induced expression of stress-responsive genes in MEFs, the transcription profiles of several mouse tissues, and leads to altered phenotypes that are not seen in mice lacking only one variant. We conclude that the compensatory binding of HMGN variants to chromatin maintains the DHS landscape, and the transcription fidelity and is necessary to retain wild-type phenotypes. Our study provides insight into mechanisms that maintain regulatory sites in chromatin and into functional compensation among nucleosome binding architectural proteins.
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Affiliation(s)
- Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Z Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Di Huang
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Marion Horsch
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Martin Klingenspor
- Molecular Nutritional Medicine, Technische Universität München, 85350 Freising, Germany; Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising, Germany
| | - Oana Amarie
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Developmental Genetics (IDG), 85764 Neuherberg, Germany
| | - Jochen Graw
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Developmental Genetics (IDG), 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Ludwig-Maximilians-Universität München, Gene Center, Institute of Molecular Animal Breeding and Biotechnology, 81377 Munich, Germany
| | - Eckhard Wolf
- Ludwig-Maximilians-Universität München, Gene Center, Institute of Molecular Animal Breeding and Biotechnology, 81377 Munich, Germany
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, 81675 Munich, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Arjan van der Velde
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Lino Tessarollo
- Neural Development Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Ivan Ovcherenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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307
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Warns JA, Davie JR, Dhasarathy A. Connecting the dots: chromatin and alternative splicing in EMT. Biochem Cell Biol 2015; 94:12-25. [PMID: 26291837 DOI: 10.1139/bcb-2015-0053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nature has devised sophisticated cellular machinery to process mRNA transcripts produced by RNA Polymerase II, removing intronic regions and connecting exons together, to produce mature RNAs. This process, known as splicing, is very closely linked to transcription. Alternative splicing, or the ability to produce different combinations of exons that are spliced together from the same genomic template, is a fundamental means of regulating protein complexity. Similar to transcription, both constitutive and alternative splicing can be regulated by chromatin and its associated factors in response to various signal transduction pathways activated by external stimuli. This regulation can vary between different cell types, and interference with these pathways can lead to changes in splicing, often resulting in aberrant cellular states and disease. The epithelial to mesenchymal transition (EMT), which leads to cancer metastasis, is influenced by alternative splicing events of chromatin remodelers and epigenetic factors such as DNA methylation and non-coding RNAs. In this review, we will discuss the role of epigenetic factors including chromatin, chromatin remodelers, DNA methyltransferases, and microRNAs in the context of alternative splicing, and discuss their potential involvement in alternative splicing during the EMT process.
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Affiliation(s)
- Jessica A Warns
- a Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, 501 N. Columbia Road Stop 9061, Grand Forks, ND 58202-9061, USA
| | - James R Davie
- b Children's Hospital Research Institute of Manitoba, John Buhler Research Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Archana Dhasarathy
- a Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, 501 N. Columbia Road Stop 9061, Grand Forks, ND 58202-9061, USA
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308
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Santhanam B, Cai H, Devreotes PN, Shaulsky G, Katoh-Kurasawa M. The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium. Nat Commun 2015; 6:7551. [PMID: 26144553 PMCID: PMC4506546 DOI: 10.1038/ncomms8551] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/20/2015] [Indexed: 12/11/2022] Open
Abstract
In many systems, including the social amoeba Dictyostelium discoideum, development is often marked by dynamic morphological and transcriptional changes orchestrated by key transcription factors. However, efforts to examine sequential genome-wide changes of gene regulation in developmental processes have been fairly limited. Here we report the developmental regulatory dynamics of GtaC, a GATA-type zinc-finger transcription factor, through the analyses of serial ChIP- and RNA-sequencing data. GtaC is essential for developmental progression, decoding extracellular cAMP pulses during early development and may play a role in mediating cell-type differentiation at later stages. We find that GtaC exhibits temporally distinctive DNA-binding patterns concordant with each developmental stage. We identify direct GtaC targets and observe cotemporaneous GtaC-binding and developmental expression regulation. Our results suggest that GtaC regulates multiple physiological processes as Dictyostelium transitions from a group of unicellular amoebae to an integrated multicellular organism. Development involves dynamic transcriptional changes. By serial ChIP- and RNA-sequencing, here, the authors show that GtaC, a GATA type transcription factor, exhibits temporally distinctive DNA binding and regulation of gene expression concordant with the development in the social amoeba Dictyostelium discoideum.
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Affiliation(s)
- Balaji Santhanam
- 1] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Huaqing Cai
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Peter N Devreotes
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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309
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Varala K, Li Y, Marshall-Colón A, Para A, Coruzzi GM. "Hit-and-Run" leaves its mark: catalyst transcription factors and chromatin modification. Bioessays 2015; 37:851-6. [PMID: 26108710 PMCID: PMC4548861 DOI: 10.1002/bies.201400205] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding how transcription factor (TF) binding is related to gene regulation is a moving target. We recently uncovered genome‐wide evidence for a “Hit‐and‐Run” model of transcription. In this model, a master TF “hits” a target promoter to initiate a rapid response to a signal. As the “hit” is transient, the model invokes recruitment of partner TFs to sustain transcription over time. Following the “run”, the master TF “hits” other targets to propagate the response genome‐wide. As such, a TF may act as a “catalyst” to mount a broad and acute response in cells that first sense the signal, while the recruited TF partners promote long‐term adaptive behavior in the whole organism. This “Hit‐and‐Run” model likely has broad relevance, as TF perturbation studies across eukaryotes show small overlaps between TF‐regulated and TF‐bound genes, implicating transient TF‐target binding. Here, we explore this “Hit‐and‐Run” model to suggest molecular mechanisms and its biological relevance.
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Affiliation(s)
- Kranthi Varala
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Ying Li
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | | | - Alessia Para
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Gloria M Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
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310
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Cirillo D, Botta-Orfila T, Tartaglia GG. By the company they keep: interaction networks define the binding ability of transcription factors. Nucleic Acids Res 2015; 43:e125. [PMID: 26089389 PMCID: PMC4627061 DOI: 10.1093/nar/gkv607] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/28/2015] [Indexed: 01/01/2023] Open
Abstract
Access to genome-wide data provides the opportunity to address questions concerning the ability of transcription factors (TFs) to assemble in distinct macromolecular complexes. Here, we introduce the PAnDA (Protein And DNA Associations) approach to characterize DNA associations with human TFs using expression profiles, protein–protein interactions and recognition motifs. Our method predicts TF binding events with >0.80 accuracy revealing cell-specific regulatory patterns that can be exploited for future investigations. Even when the precise DNA-binding motifs of a specific TF are not available, the information derived from protein-protein networks is sufficient to perform high-confidence predictions (area under the ROC curve of 0.89). PAnDA is freely available at http://service.tartaglialab.com/new_submission/panda.
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Affiliation(s)
- Davide Cirillo
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Teresa Botta-Orfila
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluís Companys, 08010 Barcelona, Spain
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311
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Faial T, Bernardo AS, Mendjan S, Diamanti E, Ortmann D, Gentsch GE, Mascetti VL, Trotter MWB, Smith JC, Pedersen RA. Brachyury and SMAD signalling collaboratively orchestrate distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells. Development 2015; 142:2121-35. [PMID: 26015544 PMCID: PMC4483767 DOI: 10.1242/dev.117838] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 04/30/2015] [Indexed: 12/17/2022]
Abstract
The transcription factor brachyury (T, BRA) is one of the first markers of gastrulation and lineage specification in vertebrates. Despite its wide use and importance in stem cell and developmental biology, its functional genomic targets in human cells are largely unknown. Here, we use differentiating human embryonic stem cells to study the role of BRA in activin A-induced endoderm and BMP4-induced mesoderm progenitors. We show that BRA has distinct genome-wide binding landscapes in these two cell populations, and that BRA interacts and collaborates with SMAD1 or SMAD2/3 signalling to regulate the expression of its target genes in a cell-specific manner. Importantly, by manipulating the levels of BRA in cells exposed to different signalling environments, we demonstrate that BRA is essential for mesoderm but not for endoderm formation. Together, our data illuminate the function of BRA in the context of human embryonic development and show that the regulatory role of BRA is context dependent. Our study reinforces the importance of analysing the functions of a transcription factor in different cellular and signalling environments.
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Affiliation(s)
- Tiago Faial
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Andreia S Bernardo
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sasha Mendjan
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Evangelia Diamanti
- Cambridge Institute for Medical Research and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0XY, UK
| | - Daniel Ortmann
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - George E Gentsch
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Victoria L Mascetti
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Matthew W B Trotter
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK
| | - James C Smith
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Roger A Pedersen
- The Anne McLaren Laboratory for Regenerative Medicine, Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
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312
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Bain DL, De Angelis RW, Connaghan KD, Yang Q, Degala GD, Lambert JR. Dissecting Steroid Receptor Function by Analytical Ultracentrifugation. Methods Enzymol 2015; 562:363-89. [PMID: 26412661 DOI: 10.1016/bs.mie.2015.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Steroid receptors comprise a family of ligand-activated transcription factors. The members include the androgen receptor (AR), estrogen receptor (ER), glucocorticoid receptor (GR), mineralocorticoid receptor (MR), and progesterone receptor (PR). Each receptor controls distinct sets of genes associated with development, metabolism, and homeostasis. Although a qualitative understanding of how individual receptors mediate gene expression has come into focus, quantitative insight remains less clear. As a step toward delineating the physical mechanisms by which individual receptors activate their target genes, we have carried out a systematic dissection of receptor interaction energetics with their multisite regulatory elements. Analytical ultracentrifugation (AUC) has proved indispensable in these studies, in part by revealing the energetics of receptor self-association and its thermodynamic coupling to DNA binding. Here, we discuss these findings in the context of understanding specificity of receptor-mediated gene control. We first highlight the role of sedimentation velocity and sedimentation equilibrium in addressing receptor assembly state, and present a comparative analysis across the receptor family. We then use these results for understanding how receptors assemble at multisite regulatory elements, and hypothesize how these findings might play a role in receptor-specific gene regulation. Finally, we examine receptor behavior in a cellular context, with a view toward linking our in vitro studies with in vivo function.
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Affiliation(s)
- David L Bain
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
| | - Rolando W De Angelis
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Keith D Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Qin Yang
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Gregory D Degala
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - James R Lambert
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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313
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Li M, Hada A, Sen P, Olufemi L, Hall MA, Smith BY, Forth S, McKnight JN, Patel A, Bowman GD, Bartholomew B, Wang MD. Dynamic regulation of transcription factors by nucleosome remodeling. eLife 2015; 4. [PMID: 26047462 PMCID: PMC4456607 DOI: 10.7554/elife.06249] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/11/2015] [Indexed: 12/27/2022] Open
Abstract
The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes. DOI:http://dx.doi.org/10.7554/eLife.06249.001 Cells contain thousands of genes that are encoded by molecules of DNA. In yeast and other eukaryotic organisms, this DNA is wrapped around proteins called histones to make structures called nucleosomes. This compacts the DNA and allows it to fit inside the tiny nucleus within the cell. The positioning of the nucleosomes influences how tightly packed the DNA is, which in turn influences the activity of genes. Less active genes tend to be found within regions of DNA that are tightly packed, while more active genes are found in less tightly packed regions. To activate a gene, proteins called transcription factors bind to a section of DNA within the gene called the promoter. Enzymes known as ‘chromatin remodelers’ can alter the locations of nucleosomes on DNA to allow the transcription factors access to the promoters of particular genes. In yeast, the SWI/SNF family of chromatin remodelers can disassemble nucleosomes to promote gene activity, while the ISW1 family organises nucleosomes into closely spaced groups to repress gene activity. However, it is not clear if, or how, chromatin remodelers can influence transcription factors that are already bound to DNA. Here, Li et al. studied the interactions between a transcription factor and the chromatin remodelers in yeast. The experiment used a piece of DNA that contained a bound transcription factor and a single nucleosome. Li et al. used a technique called ‘single molecule DNA unzipping’, which enabled them to precisely locate the position of the nucleosome and transcription factor before and after the nucleosome was remodeled. The experiments found that a chromatin remodeler called ISW1a moved the nucleosome away from the transcription factor, while a SWI/SNF chromatin remodeler moved the nucleosome towards it. Significantly, Li et al. also found that a transcription factor is a major barrier to ISW1a's remodeling activity, suggesting that ISW1a may use transcription factors as reference points to position nucleosomes. In contrast, SWI/SNF was able to slide a nucleosome past the transcription factor, which led to the transcription factor falling off the DNA. Therefore, SWI/SNF is able to move transcription factors out of the way to deactivate genes. Li et al. propose a new model for how chromatin remodelers can move nucleosomes and regulate transcription factors to alter gene activity. A future challenge will be to observe these types of activities in living cells. DOI:http://dx.doi.org/10.7554/eLife.06249.002
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Affiliation(s)
- Ming Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Arjan Hada
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Payel Sen
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Lola Olufemi
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Michael A Hall
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Benjamin Y Smith
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Scott Forth
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
| | - Jeffrey N McKnight
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Ashok Patel
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Gregory D Bowman
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Blaine Bartholomew
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, United States
| | - Michelle D Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, United States
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314
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Simon TW, Budinsky RA, Rowlands JC. A model for aryl hydrocarbon receptor-activated gene expression shows potency and efficacy changes and predicts squelching due to competition for transcription co-activators. PLoS One 2015; 10:e0127952. [PMID: 26039703 PMCID: PMC4454675 DOI: 10.1371/journal.pone.0127952] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/22/2015] [Indexed: 12/17/2022] Open
Abstract
A stochastic model of nuclear receptor-mediated transcription was developed based on activation of the aryl hydrocarbon receptor (AHR) by 2,3,7,8-tetrachlorodibenzodioxin (TCDD) and subsequent binding the activated AHR to xenobiotic response elements (XREs) on DNA. The model was based on effects observed in cells lines commonly used as in vitro experimental systems. Following ligand binding, the AHR moves into the cell nucleus and forms a heterodimer with the aryl hydrocarbon nuclear translocator (ARNT). In the model, a requirement for binding to DNA is that a generic coregulatory protein is subsequently bound to the AHR-ARNT dimer. Varying the amount of coregulator available within the nucleus altered both the potency and efficacy of TCDD for inducing for transcription of CYP1A1 mRNA, a commonly used marker for activation of the AHR. Lowering the amount of available cofactor slightly increased the EC50 for the transcriptional response without changing the efficacy or maximal response. Further reduction in the amount of cofactor reduced the efficacy and produced non-monotonic dose-response curves (NMDRCs) at higher ligand concentrations. The shapes of these NMDRCs were reminiscent of the phenomenon of squelching. Resource limitations for transcriptional machinery are becoming apparent in eukaryotic cells. Within single cells, nuclear receptor-mediated gene expression appears to be a stochastic process; however, intercellular communication and other aspects of tissue coordination may represent a compensatory process to maintain an organism’s ability to respond on a phenotypic level to various stimuli within an inconstant environment.
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Affiliation(s)
- Ted W. Simon
- Ted Simon LLC, Winston, GA, United States of America
- * E-mail:
| | - Robert A. Budinsky
- The Dow Chemical Company, Toxicology and Environmental Research & Consulting. Midland, MI, United States of America
| | - J. Craig Rowlands
- The Dow Chemical Company, Toxicology and Environmental Research & Consulting. Midland, MI, United States of America
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315
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Abstract
Since the initial recognition of the metastasis-associated protein 1 (MTA1) as a metastasis-relevant gene approximately 20 years ago, our appreciation for the complex role of the MTA family of coregulatory proteins in human cancer has profoundly grown. MTA proteins consist of six family members with similar structural units and act as central signaling nodes for integrating upstream signals into regulatory chromatin-remodeling networks, leading to regulation of gene expression in cancer cells. Substantial experimental and clinical evidence demonstrates that MTA proteins, particularly MTA1, are frequently deregulated in a wide range of human cancers. The MTA family governs cell survival, the invasive and metastatic phenotypes of cancer cells, and the aggressiveness of cancer and the prognosis of patients with MTA1 overexpressing cancers. Our discussion here highlights our current understanding of the regulatory mechanisms and functional roles of MTA proteins in cancer progression and expands upon the potential implications of MTA proteins in cancer biology and cancer therapeutics.
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Affiliation(s)
- Da-Qiang Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University, Shanghai, China; Key Laboratory of Epigenetics in Shanghai, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Rakesh Kumar
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Cellular Oncology, University of Texas M.D., Anderson Cancer Center, Houston, Texas, USA.
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316
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Charoensawan V, Martinho C, Wigge PA. "Hit-and-run": Transcription factors get caught in the act. Bioessays 2015; 37:748-54. [PMID: 26010075 DOI: 10.1002/bies.201400186] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A key challenge for understanding transcriptional regulation is being able to measure transcription factor (TF)-DNA binding events with sufficient spatial and temporal resolution; that is, when and where TFs occupy their cognate sites. A recent study by Para et al. has highlighted the dynamics underlying the activation of gene expression by a master regulator TF. This study provides concrete evidence for a long-standing hypothesis in biology, the "hit-and-run" mechanism, which was first proposed decades ago. That is, gene expression is dynamically controlled by a TF that transiently binds and activates a target gene, which might stay in a transcriptionally active state after the initial binding event has ended. Importantly, the experimental procedure introduced, TARGET, provides a useful way for identifying multiple target genes transiently bound by their regulators, which can be used in conjunction with other well-established methods to improve our understanding of transcriptional regulatory dynamics.
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Affiliation(s)
- Varodom Charoensawan
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK.,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.,Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand
| | - Claudia Martinho
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Philip A Wigge
- The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
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317
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Silva ITGD, Oliveira PSLD, Santos GM. Featuring the nucleosome surface as a therapeutic target. Trends Pharmacol Sci 2015; 36:263-9. [DOI: 10.1016/j.tips.2015.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/20/2015] [Accepted: 02/27/2015] [Indexed: 01/18/2023]
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318
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Protein Degradation of RNA Polymerase II-Association Factor 1(PAF1) Is Controlled by CNOT4 and 26S Proteasome. PLoS One 2015; 10:e0125599. [PMID: 25933433 PMCID: PMC4416890 DOI: 10.1371/journal.pone.0125599] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/24/2015] [Indexed: 12/21/2022] Open
Abstract
The PAF complex (PAFc) participates in various steps of the transcriptional process, from initiation to termination, by interacting with and recruiting various proteins to the proper locus for each step. PAFc is an evolutionarily conserved, multi-protein complex comprising PAF1, CDC73, CTR9, LEO1, yRTF1 and, in humans, hSKI8. These components of PAFc work together, and their protein levels are closely interrelated. In the present study, we investigated the mechanism of PAF1 protein degradation. We found that PAF1 protein levels are negatively regulated by the expression of CNOT4, an ortholog of yNOT4 and a member of the CCR4-NOT complex. CNOT4 specifically controls PAF1 but not other components of PAFc at the protein level by regulating the polyubiquitination of PAF1 and its subsequent degradation by the 26S proteasome. The degradation of PAF1 was found to require nuclear localization, as no PAF1 degradation by CNOT4 and the 26S proteasome was observed with NLS (nucleus localization signal)-deficient PAF1 mutants. However, chromatin binding by PAF1 was not necessary for 26S proteasome- or CNOT4-mediated degradation. Our results suggest that CNOT4 controls the degradation of chromatin-unbound PAF1 via the 26S proteasome.
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319
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Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res 2015; 46:1-30. [PMID: 25668385 PMCID: PMC4402139 DOI: 10.1016/j.preteyeres.2015.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/18/2015] [Accepted: 01/21/2015] [Indexed: 01/10/2023]
Abstract
Genomics and genetics have invaded all aspects of biology and medicine, opening uncharted territory for scientific exploration. The definition of "gene" itself has become ambiguous, and the central dogma is continuously being revised and expanded. Computational biology and computational medicine are no longer intellectual domains of the chosen few. Next generation sequencing (NGS) technology, together with novel methods of pattern recognition and network analyses, has revolutionized the way we think about fundamental biological mechanisms and cellular pathways. In this review, we discuss NGS-based genome-wide approaches that can provide deeper insights into retinal development, aging and disease pathogenesis. We first focus on gene regulatory networks (GRNs) that govern the differentiation of retinal photoreceptors and modulate adaptive response during aging. Then, we discuss NGS technology in the context of retinal disease and develop a vision for therapies based on network biology. We should emphasize that basic strategies for network construction and analyses can be transported to any tissue or cell type. We believe that specific and uniform guidelines are required for generation of genome, transcriptome and epigenome data to facilitate comparative analysis and integration of multi-dimensional data sets, and for constructing networks underlying complex biological processes. As cellular homeostasis and organismal survival are dependent on gene-gene and gene-environment interactions, we believe that network-based biology will provide the foundation for deciphering disease mechanisms and discovering novel drug targets for retinal neurodegenerative diseases.
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Affiliation(s)
- Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Tiziana Cogliati
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA.
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320
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Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling. Nat Commun 2015; 6:7048. [PMID: 25916672 DOI: 10.1038/ncomms8048] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/26/2015] [Indexed: 02/03/2023] Open
Abstract
A bimodal switch model is widely used to describe transcriptional regulation by the thyroid hormone receptor (TR). In this model, the unliganded TR forms stable, chromatin-bound complexes with transcriptional co-repressors to repress transcription. Binding of hormone dissociates co-repressors and facilitates recruitment of co-activators to activate transcription. Here we show that in addition to hormone-independent TR occupancy, ChIP-seq against endogenous TR in mouse liver tissue demonstrates considerable hormone-induced TR recruitment to chromatin associated with chromatin remodelling and activated gene transcription. Genome-wide footprinting analysis using DNase-seq provides little evidence for TR footprints both in the absence and presence of hormone, suggesting that unliganded TR engagement with repressive complexes on chromatin is, similar to activating receptor complexes, a highly dynamic process. This dynamic and ligand-dependent interaction with chromatin is likely shared by all steroid hormone receptors regardless of their capacity to repress transcription in the absence of ligand.
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321
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Garg A, Futcher B, Leatherwood J. A new transcription factor for mitosis: in Schizosaccharomyces pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression. Nucleic Acids Res 2015; 43:6874-88. [PMID: 25908789 PMCID: PMC4538799 DOI: 10.1093/nar/gkv274] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 03/18/2015] [Indexed: 12/26/2022] Open
Abstract
Mitotic genes are one of the most strongly oscillating groups of genes in the eukaryotic cell cycle. Understanding the regulation of mitotic gene expression is a key issue in cell cycle control but is poorly understood in most organisms. Here, we find a new mitotic transcription factor, Sak1, in the fission yeast Schizosaccharomyces pombe. Sak1 belongs to the RFX family of transcription factors, which have not previously been connected to cell cycle control. Sak1 binds upstream of mitotic genes in close proximity to Fkh2, a forkhead transcription factor previously implicated in regulation of mitotic genes. We show that Sak1 is the major activator of mitotic gene expression and also confirm the role of Fkh2 as the opposing repressor. Sep1, another forkhead transcription factor, is an activator for a small subset of mitotic genes involved in septation. From yeasts to humans, forkhead transcription factors are involved in mitotic gene expression and it will be interesting to see whether RFX transcription factors may also be involved in other organisms.
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Affiliation(s)
- Angad Garg
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Futcher
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Janet Leatherwood
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
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322
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Ceballos-Chávez M, Subtil-Rodríguez A, Giannopoulou EG, Soronellas D, Vázquez-Chávez E, Vicent GP, Elemento O, Beato M, Reyes JC. The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers. PLoS Genet 2015; 11:e1005174. [PMID: 25894978 PMCID: PMC4403880 DOI: 10.1371/journal.pgen.1005174] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 03/25/2015] [Indexed: 01/01/2023] Open
Abstract
While the importance of gene enhancers in transcriptional regulation is well established, the mechanisms and the protein factors that determine enhancers activity have only recently begun to be unravelled. Recent studies have shown that progesterone receptor (PR) binds regions that display typical features of gene enhancers. Here, we show by ChIP-seq experiments that the chromatin remodeler CHD8 mostly binds promoters under proliferation conditions. However, upon progestin stimulation, CHD8 re-localizes to PR enhancers also enriched in p300 and H3K4me1. Consistently, CHD8 depletion severely impairs progestin-dependent gene regulation. CHD8 binding is PR-dependent but independent of the pioneering factor FOXA1. The SWI/SNF chromatin-remodelling complex is required for PR-dependent gene activation. Interestingly, we show that CHD8 interacts with the SWI/SNF complex and that depletion of BRG1 and BRM, the ATPases of SWI/SNF complex, impairs CHD8 recruitment. We also show that CHD8 is not required for H3K27 acetylation, but contributes to increase accessibility of the enhancer to DNaseI. Furthermore, CHD8 was required for RNAPII recruiting to the enhancers and for transcription of enhancer-derived RNAs (eRNAs). Taken together our data demonstrate that CHD8 is involved in late stages of PR enhancers activation. A lot of research has been devoted during the last decades to understand the mechanisms that control gene promoters activity, however, much less is known about enhancers. Only recently, the use of genome-wide chromatin immunoprecipitation techniques has revealed the existence of more than 400,000 enhancers in the human genome. We are starting to understand the importance of these regulatory elements and how they are activated or repressed. In this work we discover that the chromatin remodeler CHD8 is recruited to Progesteron Receptor-dependent enhancers upon hormone treatment. CHD8 is required for late steps in the activation of these enhancers, including transcription of the enhancers and synthesis of eRNA (long noncoding RNAs derived form the enhancers).
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Affiliation(s)
- María Ceballos-Chávez
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Alicia Subtil-Rodríguez
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
- * E-mail: (ASR); (JCR)
| | - Eugenia G. Giannopoulou
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, New York, New York, United States of America
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, United States of America
| | - Daniel Soronellas
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elena Vázquez-Chávez
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Guillermo P. Vicent
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Olivier Elemento
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, New York, United States of America
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - José C. Reyes
- Molecular Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
- * E-mail: (ASR); (JCR)
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323
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TET3 is recruited by REST for context-specific hydroxymethylation and induction of gene expression. Cell Rep 2015; 11:283-94. [PMID: 25843715 DOI: 10.1016/j.celrep.2015.03.020] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/09/2015] [Accepted: 03/07/2015] [Indexed: 12/17/2022] Open
Abstract
Ten-eleven translocation hydroxylases (TET1-3) oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). In neurons, increased 5hmC levels within gene bodies correlate positively with gene expression. The mechanisms controlling TET activity and 5hmC levels are poorly understood. In particular, it is not known how the neuronal TET3 isoform lacking a DNA-binding domain is targeted to the DNA. To identify factors binding to TET3, we screened for proteins that co-precipitate with TET3 from mouse retina and identified the transcriptional repressor REST as a highly enriched TET3-specific interactor. REST was able to enhance TET3 hydroxylase activity after co-expression and overexpression of TET3-activated transcription of REST target genes. Moreover, we found that TET3 also interacts with NSD3 and two other H3K36 methyltransferases and is able to induce H3K36 trimethylation. We propose a mechanism for transcriptional activation in neurons that involves REST-guided targeting of TET3 to the DNA for directed 5hmC generation and NSD3-mediated H3K36 trimethylation.
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324
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Joss-Moore LA, Lane RH, Albertine KH. Epigenetic contributions to the developmental origins of adult lung disease. Biochem Cell Biol 2015; 93:119-27. [PMID: 25493710 PMCID: PMC5683896 DOI: 10.1139/bcb-2014-0093] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Perinatal insults, including intrauterine growth restriction, preterm birth, maternal exposure to toxins, or dietary deficiencies produce deviations in the epigenome of lung cells. Occurrence of perinatal insults often coincides with the final stages of lung development. The result of epigenome disruptions in response to perinatal insults during lung development may be long-term structural and functional impairment of the lung and development of lung disease. Understanding the contribution of epigenetic mechanisms to life-long lung disease following perinatal insults is the focus of the developmental origins of adult lung disease field. DNA methylation, histone modifications, and microRNA changes are all observed in various forms of lung disease. However, the perinatal contribution to such epigenetic mechanisms is poorly understood. Here we discuss the developmental origins of adult lung disease, the interplay between perinatal events, lung development and disease, and the role that epigenetic mechanisms play in connecting these events.
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Affiliation(s)
- Lisa A Joss-Moore
- Division of Neonatology, Department of Pediatrics, University of Utah, P.O. Box 581289, Salt Lake City, UT 84158, USA
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325
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Nashun B, Hill PWS, Hajkova P. Reprogramming of cell fate: epigenetic memory and the erasure of memories past. EMBO J 2015; 34:1296-308. [PMID: 25820261 PMCID: PMC4491992 DOI: 10.15252/embj.201490649] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/18/2015] [Indexed: 12/24/2022] Open
Abstract
Cell identity is a reflection of a cell type-specific gene expression profile, and consequently, cell type-specific transcription factor networks are considered to be at the heart of a given cellular phenotype. Although generally stable, cell identity can be reprogrammed in vitro by forced changes to the transcriptional network, the most dramatic example of which was shown by the induction of pluripotency in somatic cells by the ectopic expression of defined transcription factors alone. Although changes to cell fate can be achieved in this way, the efficiency of such conversion remains very low, in large part due to specific chromatin signatures constituting an epigenetic barrier to the transcription factor-mediated reprogramming processes. Here we discuss the two-way relationship between transcription factor binding and chromatin structure during cell fate reprogramming. We additionally explore the potential roles and mechanisms by which histone variants, chromatin remodelling enzymes, and histone and DNA modifications contribute to the stability of cell identity and/or provide a permissive environment for cell fate change during cellular reprogramming.
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Affiliation(s)
- Buhe Nashun
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Peter W S Hill
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Petra Hajkova
- Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, UK
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326
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Laurette P, Strub T, Koludrovic D, Keime C, Le Gras S, Seberg H, Van Otterloo E, Imrichova H, Siddaway R, Aerts S, Cornell RA, Mengus G, Davidson I. Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells. eLife 2015; 4. [PMID: 25803486 PMCID: PMC4407272 DOI: 10.7554/elife.06857] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/24/2015] [Indexed: 12/17/2022] Open
Abstract
Microphthalmia-associated transcription factor (MITF) is the master regulator of the melanocyte lineage. To understand how MITF regulates transcription, we used tandem affinity purification and mass spectrometry to define a comprehensive MITF interactome identifying novel cofactors involved in transcription, DNA replication and repair, and chromatin organisation. We show that MITF interacts with a PBAF chromatin remodelling complex comprising BRG1 and CHD7. BRG1 is essential for melanoma cell proliferation in vitro and for normal melanocyte development in vivo. MITF and SOX10 actively recruit BRG1 to a set of MITF-associated regulatory elements (MAREs) at active enhancers. Combinations of MITF, SOX10, TFAP2A, and YY1 bind between two BRG1-occupied nucleosomes thus defining both a signature of transcription factors essential for the melanocyte lineage and a specific chromatin organisation of the regulatory elements they occupy. BRG1 also regulates the dynamics of MITF genomic occupancy. MITF-BRG1 interplay thus plays an essential role in transcription regulation in melanoma.
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Affiliation(s)
- Patrick Laurette
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Thomas Strub
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Dana Koludrovic
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Céline Keime
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Stéphanie Le Gras
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Hannah Seberg
- University of Iowa College of Medicine, Iowa City, United States
| | | | - Hana Imrichova
- Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Robert Siddaway
- Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Canada
| | - Stein Aerts
- Laboratory of Computational Biology, Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Robert A Cornell
- University of Iowa College of Medicine, Iowa City, United States
| | - Gabrielle Mengus
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France
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327
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Abstract
Despite effective treatment, HIV is not completely eliminated from the infected organism because of the existence of viral reservoirs. A major reservoir consists of infected resting CD4+ T cells, mostly of memory type, that persist over time due to the stable proviral insertion and a long cellular lifespan. Resting cells do not produce viral particles and are protected from viral-induced cytotoxicity or immune killing. However, these latently infected cells can be reactivated by stochastic events or by external stimuli. The present review focuses on novel genome-wide technologies applied to the study of integration, transcriptome, and proteome characteristics and their recent contribution to the understanding of HIV latency.
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Affiliation(s)
- Angela Ciuffi
- Institute of Microbiology, University Hospital of Lausanne (CHUV), University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland,
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328
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Cunliffe VT. Experience-sensitive epigenetic mechanisms, developmental plasticity, and the biological embedding of chronic disease risk. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:53-71. [DOI: 10.1002/wsbm.1291] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 12/22/2014] [Accepted: 01/06/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Vincent T. Cunliffe
- Bateson Centre, Department of Biomedical Science; University of Sheffield; Sheffield UK
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329
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Gene regulation by H-NS as a function of growth conditions depends on chromosomal position in Escherichia coli. G3-GENES GENOMES GENETICS 2015; 5:605-14. [PMID: 25701587 PMCID: PMC4390576 DOI: 10.1534/g3.114.016139] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Cellular adaptation to changing environmental conditions requires the coordinated regulation of expression of large sets of genes by global regulatory factors such as nucleoid associated proteins. Although in eukaryotic cells genomic position is known to play an important role in regulation of gene expression, it remains to be established whether in bacterial cells there is an influence of chromosomal position on the efficiency of these global regulators. Here we show for the first time that genome position can affect transcription activity of a promoter regulated by the histone-like nucleoid-structuring protein (H-NS), a global regulator of bacterial transcription and genome organization. We have used as a local reporter of H-NS activity the level of expression of a fluorescent reporter protein under control of an H-NS−regulated promoter (Phns) at different sites along the genome. Our results show that the activity of the Phns promoter depends on whether it is placed within the AT-rich regions of the genome that are known to be bound preferentially by H-NS. This modulation of gene expression moreover depends on the growth phase and the growth rate of the cells, reflecting the changes taking place in the relative abundance of different nucleoid proteins and the inherent heterogeneous organization of the nucleoid. Genomic position can thus play a significant role in the adaptation of the cells to environmental changes, providing a fitness advantage that can explain the selection of a gene’s position during evolution.
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330
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Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40610-015-0005-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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331
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332
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Kok K, Arnosti DN. Dynamic reprogramming of chromatin: paradigmatic palimpsests and HES factors. Front Genet 2015; 6:29. [PMID: 25713582 PMCID: PMC4322839 DOI: 10.3389/fgene.2015.00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/20/2015] [Indexed: 12/02/2022] Open
Abstract
Temporal and spatial control of transcription in development is dictated to a great extent by transcriptional repressors. Some repressor complexes, such as Polycomp-group proteins, induce relatively long-term non-permissive states, whereas others such as hairy/enhancer of split (HES) family repressors are linked to dynamically modulated chromatin states associated with cycling expression of target genes. The mode of action and specificity of repressors involved in mediating this latter form of epigenetic control are unknown. Oscillating expression of HES repressors controlled by signaling pathways such as Notch suggests that the entire ensemble of HES–associated co-repressors and histone modifying complexes readily cycle on and off genes. Dynamic interactions between these factors and chromatin seem to be crucial in maintaining multipotency of progenitor cells, but the significance of such interactions in more differentiated cells is less well understood. We discuss here how genome-wide analyses and real-time gene expression measurements of HES regulated genes can help decipher the detailed mechanisms and biological importance of highly dynamic transcriptional switching mediated by epigenetic changes.
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Affiliation(s)
- Kurtulus Kok
- Genetics Program, Michigan State University , East Lansing, MI, USA
| | - David N Arnosti
- Genetics Program, Michigan State University , East Lansing, MI, USA ; Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, MI, USA
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333
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Path from schizophrenia genomics to biology: gene regulation and perturbation in neurons derived from induced pluripotent stem cells and genome editing. Neurosci Bull 2015; 31:113-27. [PMID: 25575480 DOI: 10.1007/s12264-014-1488-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 11/03/2014] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SZ) is a devastating mental disorder afflicting 1% of the population. Recent genome-wide association studies (GWASs) of SZ have identified >100 risk loci. However, the causal variants/genes and the causal mechanisms remain largely unknown, which hinders the translation of GWAS findings into disease biology and drug targets. Most risk variants are noncoding, thus likely regulate gene expression. A major mechanism of transcriptional regulation is chromatin remodeling, and open chromatin is a versatile predictor of regulatory sequences. MicroRNA-mediated post-transcriptional regulation plays an important role in SZ pathogenesis. Neurons differentiated from patient-specific induced pluripotent stem cells (iPSCs) provide an experimental model to characterize the genetic perturbation of regulatory variants that are often specific to cell type and/or developmental stage. The emerging genome-editing technology enables the creation of isogenic iPSCs and neurons to efficiently characterize the effects of SZ-associated regulatory variants on SZ-relevant molecular and cellular phenotypes involving dopaminergic, glutamatergic, and GABAergic neurotransmissions. SZ GWAS findings equipped with the emerging functional genomics approaches provide an unprecedented opportunity for understanding new disease biology and identifying novel drug targets.
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334
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Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature 2014; 518:355-359. [PMID: 25533951 PMCID: PMC4336237 DOI: 10.1038/nature13990] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 10/21/2014] [Indexed: 12/16/2022]
Abstract
Models derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signalling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells in the embryonic and adult nervous system. Here we report the transcriptional and epigenomic analysis of six consecutive neural progenitor cell stages derived from a HES5::eGFP reporter human embryonic stem cell line. Using this system, we aimed to model cell-fate decisions including specification, expansion and patterning during the ontogeny of cortical neural stem and progenitor cells. In order to dissect regulatory mechanisms that orchestrate the stage-specific differentiation process, we developed a computational framework to infer key regulators of each cell-state transition based on the progressive remodelling of the epigenetic landscape and then validated these through a pooled short hairpin RNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and suggest here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our system and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation.
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335
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Schubert V, Rudnik R, Schubert I. Chromatin associations in Arabidopsis interphase nuclei. Front Genet 2014; 5:389. [PMID: 25431580 PMCID: PMC4230181 DOI: 10.3389/fgene.2014.00389] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/23/2014] [Indexed: 11/30/2022] Open
Abstract
The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA repair. To test whether such associations are present in plants we analyzed Arabidopsis thaliana interphase nuclei by FISH using probes from different chromosomes. We found that chromatin fiber movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances. The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns. Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its 10 centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus. Nevertheless, chromatin movement enables a flexible spatial genome arrangement in plant nuclei.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben Stadt Seeland, Germany
| | - Radoslaw Rudnik
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben Stadt Seeland, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben Stadt Seeland, Germany ; Faculty of Science and Central European Institute of Technology, Masaryk University Brno, Czech Republic
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336
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Mazaira GI, Lagadari M, Erlejman AG, Galigniana MD. The Emerging Role of TPR-Domain Immunophilins in the Mechanism of Action of Steroid Receptors. NUCLEAR RECEPTOR RESEARCH 2014. [DOI: 10.11131/2014/101094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- G. I. Mazaira
- Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Lagadari
- Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
| | - A. G. Erlejman
- Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. D. Galigniana
- Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Biología y Medicina Experimental, CONICET, Buenos Aires, Argentina
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337
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Abstract
The widespread adoption of short-read DNA sequencing as a digital epigenomic readout platform has motivated the development of genome-wide tools that achieve base-pair resolution. New methods for footprinting and affinity purification of nucleosomes, RNA polymerases, chromatin remodellers and transcription factors have increased the resolution of epigenomic profiling by two orders of magnitude, leading to new insights into how the chromatin landscape affects gene regulation. These digital epigenomic tools have also been applied to directly profile both turnover kinetics and transcription in situ. In this Review, we describe how these new genome-wide tools allow interrogation of diverse aspects of the epigenome.
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338
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Lauriola M, Enuka Y, Zeisel A, D'Uva G, Roth L, Sharon-Sevilla M, Lindzen M, Sharma K, Nevo N, Feldman M, Carvalho S, Cohen-Dvashi H, Kedmi M, Ben-Chetrit N, Chen A, Solmi R, Wiemann S, Schmitt F, Domany E, Yarden Y. Diurnal suppression of EGFR signalling by glucocorticoids and implications for tumour progression and treatment. Nat Commun 2014; 5:5073. [PMID: 25278152 PMCID: PMC4205848 DOI: 10.1038/ncomms6073] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/25/2014] [Indexed: 02/07/2023] Open
Abstract
Signal transduction by receptor tyrosine kinases (RTKs) and nuclear receptors for steroid hormones is essential for body homeostasis, but the cross-talk between these receptor families is poorly understood. We observed that glucocorticoids inhibit signalling downstream of EGFR, an RTK. The underlying mechanism entails suppression of EGFR's positive feedback loops and simultaneous triggering of negative feedback loops that normally restrain EGFR. Our studies in mice reveal that the regulation of EGFR's feedback loops by glucocorticoids translates to circadian control of EGFR signalling: EGFR signals are suppressed by high glucocorticoids during the active phase (night-time in rodents), while EGFR signals are enhanced during the resting phase. Consistent with this pattern, treatment of animals bearing EGFR-driven tumours with a specific kinase inhibitor was more effective if administered during the resting phase of the day, when glucocorticoids are low. These findings support a circadian clock-based paradigm in cancer therapy.
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Affiliation(s)
- Mattia Lauriola
- 1] Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel [2] Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, Bologna 40138, Italy
| | - Yehoshua Enuka
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amit Zeisel
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gabriele D'Uva
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lee Roth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Sharon-Sevilla
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshit Lindzen
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kirti Sharma
- Division of Molecular Genome Analysis, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
| | - Nava Nevo
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Morris Feldman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Silvia Carvalho
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hadas Cohen-Dvashi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Merav Kedmi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nir Ben-Chetrit
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alon Chen
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rossella Solmi
- Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, Bologna 40138, Italy
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
| | - Fernando Schmitt
- 1] Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada M5S 1A8 [2] Department of Pathology, University Health Network, Toronto, Ontario, Canada M5G 2C4 [3] IPATIMUP, University of Porto, Porto 4200-465, Portugal
| | - Eytan Domany
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
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339
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Sung MH, Guertin MJ, Baek S, Hager GL. DNase footprint signatures are dictated by factor dynamics and DNA sequence. Mol Cell 2014; 56:275-285. [PMID: 25242143 DOI: 10.1016/j.molcel.2014.08.016] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/05/2014] [Accepted: 08/15/2014] [Indexed: 12/13/2022]
Abstract
Genomic footprinting has emerged as an unbiased discovery method for transcription factor (TF) occupancy at cognate DNA in vivo. A basic premise of footprinting is that sequence-specific TF-DNA interactions are associated with localized resistance to nucleases, leaving observable signatures of cleavage within accessible chromatin. This phenomenon is interpreted to imply protection of the critical nucleotides by the stably bound protein factor. However, this model conflicts with previous reports of many TFs exchanging with specific binding sites in living cells on a timescale of seconds. We show that TFs with short DNA residence times have no footprints at bound motif elements. Moreover, the nuclease cleavage profile within a footprint originates from the DNA sequence in the factor-binding site, rather than from the protein occupying specific nucleotides. These findings suggest a revised understanding of TF footprinting and reveal limitations in comprehensive reconstruction of the TF regulatory network using this approach.
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Affiliation(s)
- Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Michael J Guertin
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD 20892, USA.
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340
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Leung A, Parks BW, Du J, Trac C, Setten R, Chen Y, Brown K, Lusis AJ, Natarajan R, Schones DE. Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. J Biol Chem 2014; 289:23557-67. [PMID: 25006255 DOI: 10.1074/jbc.m114.581439] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Metabolic diseases result from multiple genetic and environmental factors. We report here that one manner in which environmental factors can contribute to metabolic disease progression is through modification to chromatin. We demonstrate that high fat diet leads to chromatin remodeling in the livers of C57BL/6J mice, as compared with mice fed a control diet, and that these chromatin changes are associated with changes in gene expression. We further show that the regions of greatest variation in chromatin accessibility are targeted by liver transcription factors, including HNF4α, CCAAT/enhancer-binding protein α (CEBP/α), and FOXA1. Repeating the chromatin and gene expression profiling in another mouse strain, DBA/2J, revealed that the regions of greatest chromatin change are largely strain-specific and that integration of chromatin, gene expression, and genetic data can be used to characterize regulatory regions. Our data indicate dramatic changes in the epigenome due to diet and demonstrate strain-specific dynamics in chromatin remodeling.
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Affiliation(s)
- Amy Leung
- From the Departments of Diabetes and
| | - Brian W Parks
- the Department of Medicine, UCLA, Los Angeles, California 90095
| | - Juan Du
- Cancer Biology, Beckman Research Institute and the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
| | - Candi Trac
- Cancer Biology, Beckman Research Institute and
| | - Ryan Setten
- the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
| | - Yin Chen
- the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
| | - Kevin Brown
- Cancer Biology, Beckman Research Institute and
| | - Aldons J Lusis
- the Department of Medicine, UCLA, Los Angeles, California 90095
| | - Rama Natarajan
- From the Departments of Diabetes and the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
| | - Dustin E Schones
- Cancer Biology, Beckman Research Institute and the Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, California 91010 and
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341
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Gregor T, Garcia HG, Little SC. The embryo as a laboratory: quantifying transcription in Drosophila. Trends Genet 2014; 30:364-75. [PMID: 25005921 DOI: 10.1016/j.tig.2014.06.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/08/2014] [Accepted: 06/16/2014] [Indexed: 11/16/2022]
Abstract
Transcriptional regulation of gene expression is fundamental to most cellular processes, including determination of cellular fates. Quantitative studies of transcription in cultured cells have led to significant advances in identifying mechanisms underlying transcriptional control. Recent progress allowed implementation of these same quantitative methods in multicellular organisms to ask how transcriptional regulation unfolds both in vivo and at the single molecule level in the context of embryonic development. Here we review some of these advances in early Drosophila development, which bring the embryo on par with its single celled counterparts. In particular, we discuss progress in methods to measure mRNA and protein distributions in fixed and living embryos, and we highlight some initial applications that lead to fundamental new insights about molecular transcription processes. We end with an outlook on how to further exploit the unique advantages that come with investigating transcriptional control in the multicellular context of development.
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Affiliation(s)
- Thomas Gregor
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 085444, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Hernan G Garcia
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 085444, USA
| | - Shawn C Little
- Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
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342
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Domains of genome-wide gene expression dysregulation in Down's syndrome. Nature 2014; 508:345-50. [PMID: 24740065 DOI: 10.1038/nature13200] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 03/04/2014] [Indexed: 12/27/2022]
Abstract
Trisomy 21 is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in trisomy 21, and to eliminate the noise of genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for trisomy 21. Here we show that the differential expression between the twins is organized in domains along all chromosomes that are either upregulated or downregulated. These gene expression dysregulation domains (GEDDs) can be defined by the expression level of their gene content, and are well conserved in induced pluripotent stem cells derived from the twins' fibroblasts. Comparison of the transcriptome of the Ts65Dn mouse model of Down's syndrome and normal littermate mouse fibroblasts also showed GEDDs along the mouse chromosomes that were syntenic in human. The GEDDs correlate with the lamina-associated (LADs) and replication domains of mammalian cells. The overall position of LADs was not altered in trisomic cells; however, the H3K4me3 profile of the trisomic fibroblasts was modified and accurately followed the GEDD pattern. These results indicate that the nuclear compartments of trisomic cells undergo modifications of the chromatin environment influencing the overall transcriptome, and that GEDDs may therefore contribute to some trisomy 21 phenotypes.
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343
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Siersbæk R, Baek S, Rabiee A, Nielsen R, Traynor S, Clark N, Sandelin A, Jensen ON, Sung MH, Hager GL, Mandrup S. Molecular architecture of transcription factor hotspots in early adipogenesis. Cell Rep 2014; 7:1434-1442. [PMID: 24857666 PMCID: PMC6360525 DOI: 10.1016/j.celrep.2014.04.043] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 04/02/2014] [Accepted: 04/18/2014] [Indexed: 11/19/2022] Open
Abstract
Transcription factors have recently been shown to colocalize in hotspot regions of the genome, which are further clustered into super-enhancers. However, the detailed molecular organization of transcription factors at hotspot regions is poorly defined. Here, we have used digital genomic footprinting to precisely define factor localization at a genome-wide level during the early phase of 3T3-L1 adipocyte differentiation, which allows us to obtain detailed molecular insight into how transcription factors target hotspots. We demonstrate the formation of ATF-C/EBP heterodimers at a composite motif on chromatin, and we suggest that this may be a general mechanism for integrating external signals on chromatin. Furthermore, we find evidence of extensive recruitment of transcription factors to hotspots through alternative mechanisms not involving their known motifs and demonstrate that these alternative binding events are functionally important for hotspot formation and activity. Taken together, these findings provide a framework for understanding transcription factor cooperativity in hotspots.
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Affiliation(s)
- Rasmus Siersbæk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Atefeh Rabiee
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Sofie Traynor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Nicholas Clark
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
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344
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Groeneweg FL, van Royen ME, Fenz S, Keizer VIP, Geverts B, Prins J, de Kloet ER, Houtsmuller AB, Schmidt TS, Schaaf MJM. Quantitation of glucocorticoid receptor DNA-binding dynamics by single-molecule microscopy and FRAP. PLoS One 2014; 9:e90532. [PMID: 24632838 PMCID: PMC3954550 DOI: 10.1371/journal.pone.0090532] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 02/02/2014] [Indexed: 02/01/2023] Open
Abstract
Recent advances in live cell imaging have provided a wealth of data on the dynamics of transcription factors. However, a consistent quantitative description of these dynamics, explaining how transcription factors find their target sequences in the vast amount of DNA inside the nucleus, is still lacking. In the present study, we have combined two quantitative imaging methods, single-molecule microscopy and fluorescence recovery after photobleaching, to determine the mobility pattern of the glucocorticoid receptor (GR) and the mineralocorticoid receptor (MR), two ligand-activated transcription factors. For dexamethasone-activated GR, both techniques showed that approximately half of the population is freely diffusing, while the remaining population is bound to DNA. Of this DNA-bound population about half the GRs appeared to be bound for short periods of time (∼ 0.7 s) and the other half for longer time periods (∼ 2.3 s). A similar pattern of mobility was seen for the MR activated by aldosterone. Inactive receptors (mutant or antagonist-bound receptors) show a decreased DNA binding frequency and duration, but also a higher mobility for the diffusing population. Likely, very brief (≤ 1 ms) interactions with DNA induced by the agonists underlie this difference in diffusion behavior. Surprisingly, different agonists also induce different mobilities of both receptors, presumably due to differences in ligand-induced conformational changes and receptor complex formation. In summary, our data provide a consistent quantitative model of the dynamics of GR and MR, indicating three types of interactions with DNA, which fit into a model in which frequent low-affinity DNA binding facilitates the search for high-affinity target sequences.
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Affiliation(s)
- Femke L. Groeneweg
- Department of Medical Pharmacology, Leiden University/LUMC, Leiden, The Netherlands
| | | | - Susanne Fenz
- Physics of Life Processes, Institute of Physics (LION), Leiden University, Leiden, The Netherlands
- Cell & Developmental Biology, Biocenter, Würzburg University, Würzburg, Germany
| | - Veer I. P. Keizer
- Molecular Cell Biology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Bart Geverts
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Jurrien Prins
- Department of Medical Pharmacology, Leiden University/LUMC, Leiden, The Netherlands
- Molecular Cell Biology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - E. Ron de Kloet
- Department of Medical Pharmacology, Leiden University/LUMC, Leiden, The Netherlands
| | | | - Thomas S. Schmidt
- Physics of Life Processes, Institute of Physics (LION), Leiden University, Leiden, The Netherlands
| | - Marcel J. M. Schaaf
- Molecular Cell Biology, Institute of Biology, Leiden University, Leiden, The Netherlands
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