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Brunelle M, Nordell Markovits A, Rodrigue S, Lupien M, Jacques PÉ, Gévry N. The histone variant H2A.Z is an important regulator of enhancer activity. Nucleic Acids Res 2015; 43:9742-56. [PMID: 26319018 PMCID: PMC4787790 DOI: 10.1093/nar/gkv825] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 07/15/2015] [Accepted: 08/03/2015] [Indexed: 12/11/2022] Open
Abstract
Gene regulatory programs in different cell types are largely defined through cell-specific enhancers activity. The histone variant H2A.Z has been shown to play important roles in transcription mainly by controlling proximal promoters, but its effect on enhancer functions remains unclear. Here, we demonstrate by genome-wide approaches that H2A.Z is present at a subset of active enhancers bound by the estrogen receptor alpha (ERα). We also determine that H2A.Z does not influence the local nucleosome positioning around ERα enhancers using ChIP sequencing at nucleosomal resolution and unsupervised pattern discovery. We further highlight that H2A.Z-enriched enhancers are associated with chromatin accessibility, H3K122ac enrichment and hypomethylated DNA. Moreover, upon estrogen stimulation, the enhancers occupied by H2A.Z produce enhancer RNAs (eRNAs), and recruit RNA polymerase II as well as RAD21, a member of the cohesin complex involved in chromatin interactions between enhancers and promoters. Importantly, their recruitment and eRNAs production are abolished by H2A.Z depletion, thereby revealing a novel functional link between H2A.Z occupancy and enhancer activity. Taken together, our findings suggest that H2A.Z acts as an important player for enhancer functions by establishing and maintaining a chromatin environment required for RNA polymerase II recruitment, eRNAs transcription and enhancer-promoters interactions, all essential attributes of enhancer activity.
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Affiliation(s)
- Mylène Brunelle
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada
| | - Alexei Nordell Markovits
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada Ontario Cancer Institute, Princess Margaret Cancer Centre/University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada
| | - Mathieu Lupien
- Département d'informatique, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada
| | - Pierre-Étienne Jacques
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada Ontario Cancer Institute, Princess Margaret Cancer Centre/University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada Centre de recherche du Centre hospitalier universitaire de Sherbrooke, 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Nicolas Gévry
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada
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152
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Li J, Drubay D, Michiels S, Gautheret D. Mining the coding and non-coding genome for cancer drivers. Cancer Lett 2015; 369:307-15. [PMID: 26433158 DOI: 10.1016/j.canlet.2015.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/24/2015] [Accepted: 09/24/2015] [Indexed: 12/20/2022]
Abstract
Progress in next-generation sequencing provides unprecedented opportunities to fully characterize the spectrum of somatic mutations of cancer genomes. Given the large number of somatic mutations identified by such technologies, the prioritization of cancer-driving events is a consistent bottleneck. Most bioinformatics tools concentrate on driver mutations in the coding fraction of the genome, those causing changes in protein products. As more non-coding pathogenic variants are identified and characterized, the development of computational approaches to effectively prioritize cancer-driving variants within the non-coding fraction of human genome is becoming critical. After a short summary of methods for coding variant prioritization, we here review the highly diverse non-coding elements that may act as cancer drivers and describe recent methods that attempt to evaluate the deleteriousness of sequence variation in these elements. With such tools, the prioritization and identification of cancer-implicated regulatory elements and non-coding RNAs is becoming a reality.
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Affiliation(s)
- Jia Li
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Damien Drubay
- Service de Biostatistique et d'Epidemiologie, Gustave Roussy, Villejuif, France; INSERM U1018, CESP, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Stefan Michiels
- Service de Biostatistique et d'Epidemiologie, Gustave Roussy, Villejuif, France; INSERM U1018, CESP, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France.
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153
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Tissue-Specific Enrichment of Lymphoma Risk Loci in Regulatory Elements. PLoS One 2015; 10:e0139360. [PMID: 26422229 PMCID: PMC4589387 DOI: 10.1371/journal.pone.0139360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/10/2015] [Indexed: 11/19/2022] Open
Abstract
Though numerous polymorphisms have been associated with risk of developing lymphoma, how these variants function to promote tumorigenesis is poorly understood. Here, we report that lymphoma risk SNPs, especially in the non-Hodgkin's lymphoma subtype chronic lymphocytic leukemia, are significantly enriched for co-localization with epigenetic marks of active gene regulation. These enrichments were seen in a lymphoid-specific manner for numerous ENCODE datasets, including DNase-hypersensitivity as well as multiple segmentation-defined enhancer regions. Furthermore, we identify putatively functional SNPs that are both in regulatory elements in lymphocytes and are associated with gene expression changes in blood. We developed an algorithm, UES, that uses a Monte Carlo simulation approach to calculate the enrichment of previously identified risk SNPs in various functional elements. This multiscale approach integrating multiple datasets helps disentangle the underlying biology of lymphoma, and more broadly, is generally applicable to GWAS results from other diseases as well.
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154
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Higgins GA, Allyn-Feuer A, Athey BD. Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response. Pharmacogenomics 2015; 16:1565-83. [PMID: 26340055 DOI: 10.2217/pgs.15.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
AIM To provide insight into potential regulatory mechanisms of gene expression underlying addiction, analgesia, psychotropic drug response and adverse drug events, genome-wide association studies searching for variants associated with these phenotypes has been undertaken with limited success. We undertook analysis of these results with the aim of applying epigenetic knowledge to aid variant discovery and interpretation. METHODS We applied conditional imputation to results from 26 genome-wide association studies and three candidate gene-association studies. The analysis workflow included data from chromatin conformation capture, chromatin state annotation, DNase I hypersensitivity, hypomethylation, anatomical localization and biochronicity. We also made use of chromatin state data from the epigenome roadmap, transcription factor-binding data, spatial maps from published Hi-C datasets and 'guilt by association' methods. RESULTS We identified 31 pharmacoepigenomic SNPs from a total of 2024 variants in linkage disequilibrium with lead SNPs, of which only 6% were coding variants. Interrogation of chromatin state using our workflow and the epigenome roadmap showed agreement on 34 of 35 tissue assignments to regulatory elements including enhancers and promoters. Loop boundary domains were inferred by association with CTCF (CCCTC-binding factor) and cohesin, suggesting proximity to topologically associating domain boundaries and enhancer clusters. Spatial interactions between enhancer-promoter pairs detected both known and previously unknown mechanisms. Addiction and analgesia SNPs were common in relevant populations and exhibited large effect sizes, whereas a SNP located in the promoter of the SLC1A2 gene exhibited a moderate effect size for lithium response in bipolar disorder in patients of European ancestry. SNPs associated with drug-induced organ injury were rare but exhibited the largest effect sizes, consistent with the published literature. CONCLUSION This work demonstrates that an in silico bioinformatics-based approach using integrative analysis of a diversity of molecular and morphological data types can discover pharmacoepigenomic variants that are suitable candidates for further validation in cell lines, animal models and human clinical trials.
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Affiliation(s)
- Gerald A Higgins
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, 1301 Catherine Road, Ann Arbor, MI 48109, USA
- Pharmacogenomic Science, Assurex Health, Inc., Mason, OH, USA
| | - Ari Allyn-Feuer
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, 1301 Catherine Road, Ann Arbor, MI 48109, USA
| | - Brian D Athey
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, 1301 Catherine Road, Ann Arbor, MI 48109, USA
- Department of Psychiatry, University of Michigan Medical School, Ann Arbor, MI, USA
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155
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Bowman SK. Discovering enhancers by mapping chromatin features in primary tissue. Genomics 2015; 106:140-144. [DOI: 10.1016/j.ygeno.2015.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/04/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
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156
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Nalabothula N, Al-jumaily T, Eteleeb AM, Flight RM, Xiaorong S, Moseley H, Rouchka EC, Fondufe-Mittendorf YN. Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation. PLoS One 2015; 10:e0135410. [PMID: 26305327 PMCID: PMC4549251 DOI: 10.1371/journal.pone.0135410] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/21/2015] [Indexed: 12/22/2022] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear enzyme involved in DNA repair, chromatin remodeling and gene expression. PARP1 interactions with chromatin architectural multi-protein complexes (i.e. nucleosomes) alter chromatin structure resulting in changes in gene expression. Chromatin structure impacts gene regulatory processes including transcription, splicing, DNA repair, replication and recombination. It is important to delineate whether PARP1 randomly associates with nucleosomes or is present at specific nucleosome regions throughout the cell genome. We performed genome-wide association studies in breast cancer cell lines to address these questions. Our studies show that PARP1 associates with epigenetic regulatory elements genome-wide, such as active histone marks, CTCF and DNase hypersensitive sites. Additionally, the binding of PARP1 to chromatin genome-wide is mutually exclusive with DNA methylation pattern suggesting a functional interplay between PARP1 and DNA methylation. Indeed, inhibition of PARylation results in genome-wide changes in DNA methylation patterns. Our results suggest that PARP1 controls the fidelity of gene transcription and marks actively transcribed gene regions by selectively binding to transcriptionally active chromatin. These studies provide a platform for developing our understanding of PARP1’s role in gene regulation.
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Affiliation(s)
- Narasimharao Nalabothula
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Taha Al-jumaily
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Abdallah M. Eteleeb
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Robert M. Flight
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Shao Xiaorong
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Hunter Moseley
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, United States of America
| | - Yvonne N. Fondufe-Mittendorf
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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157
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Bilgin Sonay T, Carvalho T, Robinson MD, Greminger MP, Krützen M, Comas D, Highnam G, Mittelman D, Sharp A, Marques-Bonet T, Wagner A. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. Genome Res 2015; 25:1591-9. [PMID: 26290536 PMCID: PMC4617956 DOI: 10.1101/gr.190868.115] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 08/14/2015] [Indexed: 12/20/2022]
Abstract
Tandem repeats (TRs) are stretches of DNA that are highly variable in length and mutate rapidly. They are thus an important source of genetic variation. This variation is highly informative for population and conservation genetics. It has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation in humans and closely related species have been scarce due to technical difficulties derived from short-read technology. Here we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, in a total of six different species, and studied their impact on gene expression evolution. We found that population diversity patterns can be efficiently captured with short TRs (repeat unit length, 1–5 bp). We examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length, 2–50 bp). Genes that contained TRs in the promoters, in their 3′ untranslated region, in introns, and in exons had higher expression divergence than genes without repeats in the regions. Polymorphic small repeats (1–5 bp) had also higher expression divergence compared with genes with fixed or no TRs in the gene promoters. Our findings highlight the potential contribution of TRs to human evolution through gene regulation.
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Affiliation(s)
- Tugce Bilgin Sonay
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-805 Zurich, Switzerland; The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tiago Carvalho
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Mark D Robinson
- The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Maja P Greminger
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, CH-8057 Zurich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Anthropological Institute and Museum, University of Zurich, CH-8057 Zurich, Switzerland
| | - David Comas
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gareth Highnam
- Department of Biological Science and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - David Mittelman
- Department of Biological Science and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Andrew Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai School, New York, New York 10029, USA
| | - Tomàs Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, 08028 Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-805 Zurich, Switzerland; The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; The Santa Fe Institute, Santa Fe, New Mexico 87501, USA
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158
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Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape. Nat Rev Immunol 2015; 15:585-94. [DOI: 10.1038/nri3884] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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159
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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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160
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Chromatin Dynamics in the Regulation of CFTR Expression. Genes (Basel) 2015; 6:543-58. [PMID: 26184320 PMCID: PMC4584316 DOI: 10.3390/genes6030543] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 12/31/2022] Open
Abstract
The contribution of chromatin dynamics to the regulation of human disease-associated loci such as the cystic fibrosis transmembrane conductance regulator (CFTR) gene has been the focus of intensive experimentation for many years. Recent technological advances in the analysis of transcriptional mechanisms across the entire human genome have greatly facilitated these studies. In this review we describe the complex machinery of tissue-specific regulation of CFTR expression, and put earlier observations in context by incorporating them into datasets generated by the most recent genomics methods. Though the gene promoter is required for CFTR expression, cell-type specific regulatory elements are located elsewhere in the gene and in flanking intergenic regions. Probably within its own topological domain established by the architectural proteins CTCF and cohesin, the CFTR locus utilizes chromatin dynamics to remodel nucleosomes, recruit cell-selective transcription factors, and activate intronic enhancers. These cis-acting elements are then brought to the gene promoter by chromatin looping mechanisms, which establish long-range interactions across the locus. Despite its complexity, the CFTR locus provides a paradigm for elucidating the critical role of chromatin dynamics in the transcription of individual human genes.
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161
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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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162
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From Structural Variation of Gene Molecules to Chromatin Dynamics and Transcriptional Bursting. Genes (Basel) 2015; 6:469-83. [PMID: 26136240 PMCID: PMC4584311 DOI: 10.3390/genes6030469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/08/2015] [Accepted: 06/24/2015] [Indexed: 12/19/2022] Open
Abstract
Transcriptional activation of eukaryotic genes is accompanied, in general, by a change in the sensitivity of promoter chromatin to endonucleases. The structural basis of this alteration has remained elusive for decades; but the change has been viewed as a transformation of one structure into another, from "closed" to "open" chromatin. In contradistinction to this static and deterministic view of the problem, a dynamical and probabilistic theory of promoter chromatin has emerged as its solution. This theory, which we review here, explains observed variation in promoter chromatin structure at the level of single gene molecules and provides a molecular basis for random bursting in transcription-the conjecture that promoters stochastically transition between transcriptionally conducive and inconducive states. The mechanism of transcriptional regulation may be understood only in probabilistic terms.
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163
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Dailey L. High throughput technologies for the functional discovery of mammalian enhancers: new approaches for understanding transcriptional regulatory network dynamics. Genomics 2015; 106:151-158. [PMID: 26072436 DOI: 10.1016/j.ygeno.2015.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/18/2015] [Accepted: 06/08/2015] [Indexed: 01/08/2023]
Abstract
Completion of the human and mouse genomes has inspired new initiatives to obtain a global understanding of the functional regulatory networks governing gene expression. Enhancers are primary regulatory DNA elements determining precise spatio- and temporal gene expression patterns, but the observation that they can function at any distance from the gene(s) they regulate has made their genome-wide characterization challenging. Since traditional, single reporter approaches would be unable to accomplish this enormous task, high throughput technologies for mapping chromatin features associated with enhancers have emerged as an effective surrogate for enhancer discovery. However, the last few years have witnessed the development of several new innovative approaches that can effectively screen for and discover enhancers based on their functional activation of transcription using massively parallel reporter systems. In addition to their application for genome annotation, these new high throughput functional approaches open new and exciting avenues for modeling gene regulatory networks.
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Affiliation(s)
- Lisa Dailey
- NYU School of Medicine, Department of Microbiology, Kimmel Center for Stem Cell Biology, 550 First Avenue, MSB 252, New York, NY 10016, United States.
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164
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Liu MJ, Seddon AE, Tsai ZTY, Major IT, Floer M, Howe GA, Shiu SH. Determinants of nucleosome positioning and their influence on plant gene expression. Genome Res 2015; 25:1182-95. [PMID: 26063739 PMCID: PMC4510002 DOI: 10.1101/gr.188680.114] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 06/10/2015] [Indexed: 01/05/2023]
Abstract
Nucleosome positioning influences the access of transcription factors (TFs) to their binding sites and gene expression. Studies in plant, animal, and fungal models demonstrate similar nucleosome positioning patterns along genes and correlations between occupancy and expression. However, the relationships among nucleosome positioning, cis-regulatory element accessibility, and gene expression in plants remain undefined. Here we showed that plant nucleosome depletion occurs on specific 6-mer motifs and this sequence-specific nucleosome depletion is predictive of expression levels. Nucleosome-depleted regions in Arabidopsis thaliana tend to have higher G/C content, unlike yeast, and are centered on specific G/C-rich 6-mers, suggesting that intrinsic sequence properties, such as G/C content, cannot fully explain plant nucleosome positioning. These 6-mer motif sites showed higher DNase I hypersensitivity and are flanked by strongly phased nucleosomes, consistent with known TF binding sites. Intriguingly, this 6-mer-specific nucleosome depletion pattern occurs not only in promoter but also in genic regions and is significantly correlated with higher gene expression level, a phenomenon also found in rice but not in yeast. Among the 6-mer motifs enriched in genes responsive to treatment with the defense hormone jasmonate, there are no significant changes in nucleosome occupancy, suggesting that these sites are potentially preconditioned to enable rapid response without changing chromatin state significantly. Our study provides a global assessment of the joint contribution of nucleosome occupancy and motif sequences that are likely cis-elements to the control of gene expression in plants. Our findings pave the way for further understanding the impact of chromatin state on plant transcriptional regulatory circuits.
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Affiliation(s)
- Ming-Jung Liu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Alexander E Seddon
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Zing Tsung-Yeh Tsai
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Ian T Major
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - Monique Floer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Gregg A Howe
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
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165
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Stavreva DA, Coulon A, Baek S, Sung MH, John S, Stixova L, Tesikova M, Hakim O, Miranda T, Hawkins M, Stamatoyannopoulos JA, Chow CC, Hager GL. Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing. Genome Res 2015; 25:845-57. [PMID: 25677181 PMCID: PMC4448681 DOI: 10.1101/gr.184168.114] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/05/2015] [Indexed: 12/20/2022]
Abstract
Although physiological steroid levels are often pulsatile (ultradian), the genomic effects of this pulsatility are poorly understood. By utilizing glucocorticoid receptor (GR) signaling as a model system, we uncovered striking spatiotemporal relationships between receptor loading, lifetimes of the DNase I hypersensitivity sites (DHSs), long-range interactions, and gene regulation. We found that hormone-induced DHSs were enriched within ± 50 kb of GR-responsive genes and displayed a broad spectrum of lifetimes upon hormone withdrawal. These lifetimes dictate the strength of the DHS interactions with gene targets and contribute to gene regulation from a distance. Our results demonstrate that pulsatile and constant hormone stimulations induce unique, treatment-specific patterns of gene and regulatory element activation. These modes of activation have implications for corticosteroid function in vivo and for steroid therapies in various clinical settings.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Antoine Coulon
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Sam John
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Lenka Stixova
- Department of Molecular Cytology and Cytometry, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
| | - Martina Tesikova
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Tina Miranda
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Mary Hawkins
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | | | - Carson C Chow
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
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166
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Kotomura N, Harada N, Ishihara S. The Proportion of Chromatin Graded between Closed and Open States Determines the Level of Transcripts Derived from Distinct Promoters in the CYP19 Gene. PLoS One 2015; 10:e0128282. [PMID: 26020632 PMCID: PMC4447357 DOI: 10.1371/journal.pone.0128282] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 04/23/2015] [Indexed: 11/19/2022] Open
Abstract
The human CYP19 gene encodes aromatase, which converts androgens to estrogens. CYP19 mRNA variants are transcribed mainly from three promoters. Quantitative RT-PCR was used to measure the relative amounts of each of the three transcripts and determine the on/off state of the promoters. While some of the promoters were silent, CYP19 mRNA production differed among the other promoters, whose estimated transcription levels were 0.001% to 0.1% of that of the TUBB control gene. To investigate the structural aspects of chromatin that were responsible for this wide range of activity of the CYP19 promoters, we used a fractionation protocol, designated SEVENS, which sequentially separates densely packed nucleosomes from dispersed nucleosomes. The fractional distribution of each inactive promoter showed a similar pattern to that of the repressed reference loci; the inactive regions were distributed toward lower fractions, in which closed chromatin comprising packed nucleosomes was enriched. In contrast, active CYP19 promoters were raised toward upper fractions, including dispersed nucleosomes in open chromatin. Importantly, these active promoters were moderately enriched in the upper fractions as compared to active reference loci, such as the TUBB promoter; the proportion of open chromatin appeared to be positively correlated to the promoter strength. These results, together with ectopic transcription accompanied by an increase in the proportion of open chromatin in cells treated with an H3K27me inhibitor, indicate that CYP19 mRNA could be transcribed from a promoter in which chromatin is shifted toward an open state in the equilibrium between closed and open chromatin.
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Affiliation(s)
- Naoe Kotomura
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Nobuhiro Harada
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Satoru Ishihara
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- * E-mail:
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167
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Wang C, Lv Y, Wang B, Yin C, Lin Y, Pan L. Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale. Nucleic Acids Res 2015; 43:4429-46. [PMID: 25883143 PMCID: PMC4482085 DOI: 10.1093/nar/gkv334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 03/31/2015] [Indexed: 01/23/2023] Open
Abstract
The genome-scale delineation of in vivo protein–DNA interactions is key to understanding genome function. Only ∼5% of transcription factors (TFs) in the Aspergillus genus have been identified using traditional methods. Although the Aspergillus oryzae genome contains >600 TFs, knowledge of the in vivo genome-wide TF-binding sites (TFBSs) in aspergilli remains limited because of the lack of high-quality antibodies. We investigated the landscape of in vivo protein–DNA interactions across the A. oryzae genome through coupling the DNase I digestion of intact nuclei with massively parallel sequencing and the analysis of cleavage patterns in protein–DNA interactions at single-nucleotide resolution. The resulting map identified overrepresented de novo TF-binding motifs from genomic footprints, and provided the detailed chromatin remodeling patterns and the distribution of digital footprints near transcription start sites. The TFBSs of 19 known Aspergillus TFs were also identified based on DNase I digestion data surrounding potential binding sites in conjunction with TF binding specificity information. We observed that the cleavage patterns of TFBSs were dependent on the orientation of TF motifs and independent of strand orientation, consistent with the DNA shape features of binding motifs with flanking sequences.
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Affiliation(s)
- Chao Wang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Yangyong Lv
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Bin Wang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Chao Yin
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Ying Lin
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Li Pan
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
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168
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Risca VI, Greenleaf WJ. Unraveling the 3D genome: genomics tools for multiscale exploration. Trends Genet 2015; 31:357-72. [PMID: 25887733 DOI: 10.1016/j.tig.2015.03.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/16/2015] [Accepted: 03/24/2015] [Indexed: 12/15/2022]
Abstract
A decade of rapid method development has begun to yield exciting insights into the 3D architecture of the metazoan genome and the roles it may play in regulating transcription. Here we review core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.
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Affiliation(s)
- Viviana I Risca
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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169
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Jablonka E, Lamb MJ. The inheritance of acquired epigenetic variations: Table 1. Int J Epidemiol 2015; 44:1094-103. [DOI: 10.1093/ije/dyv020] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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170
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Jiang J. The 'dark matter' in the plant genomes: non-coding and unannotated DNA sequences associated with open chromatin. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:17-23. [PMID: 25625239 DOI: 10.1016/j.pbi.2015.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 05/03/2023]
Abstract
Sequencing of complete plant genomes has become increasingly more routine since the advent of the next-generation sequencing technology. Identification and annotation of large amounts of noncoding but functional DNA sequences, including cis-regulatory DNA elements (CREs), have become a new frontier in plant genome research. Genomic regions containing active CREs bound to regulatory proteins are hypersensitive to DNase I digestion and are called DNase I hypersensitive sites (DHSs). Several recent DHS studies in plants illustrate that DHS datasets produced by DNase I digestion followed by next-generation sequencing (DNase-seq) are highly valuable for the identification and characterization of CREs associated with plant development and responses to environmental cues. DHS-based genomic profiling has opened a door to identify and annotate the 'dark matter' in sequenced plant genomes.
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Affiliation(s)
- Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
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171
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Abstract
INTRODUCTION Regulation of gene expression involves a variety of mechanisms driven by a complex regulatory network of factors. Control of transcription is an important step in gene expression regulation, which integrates the function of cis-acting and trans-acting elements. Among cis-regulatory elements, enhancer RNA (eRNA)-producing domains recently emerged as widespread and potent regulators of transcription and cell fate decision. Thus, manipulation of eRNA levels becomes a novel and appealing avenue for the design of new therapeutic treatments. AREAS COVERED In this review, we focus on eRNA-producing domains. We describe mechanisms involved in their cell-type specific selection and activation as well as their epigenetic features. In addition, we present their function and the growing evidences of their deregulation in human diseases. Finally, we discuss eRNAs as potential therapeutic targets. EXPERT OPINION As key factors in the control of transcription, eRNAs appear to possess a great potential for the establishment of new therapy options. However, thorough testing as well as providing the genetic toolbox to target eRNAs will be needed to fully assess the practical and clinical possibilities.
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Affiliation(s)
- Nicolas Léveillé
- The Netherlands Cancer Institute, Division of Biological Stress Response , Plesmanlaan 121, 1066 CX, Amsterdam , The Netherlands
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172
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Pazin MJ. Using the ENCODE Resource for Functional Annotation of Genetic Variants. Cold Spring Harb Protoc 2015; 2015:522-36. [PMID: 25762420 DOI: 10.1101/pdb.top084988] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article illustrates the use of the Encyclopedia of DNA Elements (ENCODE) resource to generate or refine hypotheses from genomic data on disease and other phenotypic traits. First, the goals and history of ENCODE and related epigenomics projects are reviewed. Second, the rationale for ENCODE and the major data types used by ENCODE are briefly described, as are some standard heuristics for their interpretation. Third, the use of the ENCODE resource is examined. Standard use cases for ENCODE, accessing the ENCODE resource, and accessing data from related projects are discussed. Although the focus of this article is the use of ENCODE data, some of the same approaches can be used with data from other projects.
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Affiliation(s)
- Michael J Pazin
- Division of Genome Sciences, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
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173
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Suryamohan K, Halfon MS. Identifying transcriptional cis-regulatory modules in animal genomes. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015; 4:59-84. [PMID: 25704908 PMCID: PMC4339228 DOI: 10.1002/wdev.168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/04/2014] [Accepted: 11/16/2014] [Indexed: 11/08/2022]
Abstract
UNLABELLED Gene expression is regulated through the activity of transcription factors (TFs) and chromatin-modifying proteins acting on specific DNA sequences, referred to as cis-regulatory elements. These include promoters, located at the transcription initiation sites of genes, and a variety of distal cis-regulatory modules (CRMs), the most common of which are transcriptional enhancers. Because regulated gene expression is fundamental to cell differentiation and acquisition of new cell fates, identifying, characterizing, and understanding the mechanisms of action of CRMs is critical for understanding development. CRM discovery has historically been challenging, as CRMs can be located far from the genes they regulate, have few readily identifiable sequence characteristics, and for many years were not amenable to high-throughput discovery methods. However, the recent availability of complete genome sequences and the development of next-generation sequencing methods have led to an explosion of both computational and empirical methods for CRM discovery in model and nonmodel organisms alike. Experimentally, CRMs can be identified through chromatin immunoprecipitation directed against TFs or histone post-translational modifications, identification of nucleosome-depleted 'open' chromatin regions, or sequencing-based high-throughput functional screening. Computational methods include comparative genomics, clustering of known or predicted TF-binding sites, and supervised machine-learning approaches trained on known CRMs. All of these methods have proven effective for CRM discovery, but each has its own considerations and limitations, and each is subject to a greater or lesser number of false-positive identifications. Experimental confirmation of predictions is essential, although shortcomings in current methods suggest that additional means of validation need to be developed. For further resources related to this article, please visit the WIREs website. CONFLICT OF INTEREST The authors have declared no conflicts of interest for this article.
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Affiliation(s)
- Kushal Suryamohan
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
| | - Marc S. Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
- NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA
- Molecular and Cellular Biology Department and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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174
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An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape. Sci Rep 2015; 5:8465. [PMID: 25682954 PMCID: PMC4329551 DOI: 10.1038/srep08465] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/21/2015] [Indexed: 12/12/2022] Open
Abstract
DNase I hypersensitive sites (DHSs) define the accessible chromatin landscape and have revolutionised the discovery of distinct cis-regulatory elements in diverse organisms. Here, we report the first comprehensive map of human transcription factor binding site (TFBS)-clustered regions using Gaussian kernel density estimation based on genome-wide mapping of the TFBSs in 133 human cell and tissue types. Approximately 1.6 million distinct TFBS-clustered regions, collectively spanning 27.7% of the human genome, were discovered. The TFBS complexity assigned to each TFBS-clustered region was highly correlated with genomic location, cell selectivity, evolutionary conservation, sequence features, and functional roles. An integrative analysis of these regions using ENCODE data revealed transcription factor occupancy, transcriptional activity, histone modification, DNA methylation, and chromatin structures that varied based on TFBS complexity. Furthermore, we found that we could recreate lineage-branching relationships by simple clustering of the TFBS-clustered regions from terminally differentiated cells. Based on these findings, a model of transcriptional regulation determined by TFBS complexity is proposed.
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175
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Lavin Y, Winter D, Blecher-Gonen R, David E, Keren-Shaul H, Merad M, Jung S, Amit I. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell 2015; 159:1312-26. [PMID: 25480296 DOI: 10.1016/j.cell.2014.11.018] [Citation(s) in RCA: 1499] [Impact Index Per Article: 166.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/11/2014] [Accepted: 11/11/2014] [Indexed: 02/09/2023]
Abstract
Macrophages are critical for innate immune defense and also control organ homeostasis in a tissue-specific manner. They provide a fitting model to study the impact of ontogeny and microenvironment on chromatin state and whether chromatin modifications contribute to macrophage identity. Here, we profile the dynamics of four histone modifications across seven tissue-resident macrophage populations. We identify 12,743 macrophage-specific enhancers and establish that tissue-resident macrophages have distinct enhancer landscapes beyond what can be explained by developmental origin. Combining our enhancer catalog with gene expression profiles and open chromatin regions, we show that a combination of tissue- and lineage-specific transcription factors form the regulatory networks controlling chromatin specification in tissue-resident macrophages. The environment is capable of shaping the chromatin landscape of transplanted bone marrow precursors, and even differentiated macrophages can be reprogrammed when transferred into a new microenvironment. These results provide a comprehensive view of macrophage regulatory landscape and highlight the importance of the microenvironment, along with pioneer factors in orchestrating identity and plasticity.
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Affiliation(s)
- Yonit Lavin
- Department of Oncological Sciences, Immunology Institute and the Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deborah Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miriam Merad
- Department of Oncological Sciences, Immunology Institute and the Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
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176
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Baranello L, Kouzine F, Levens D. DNA topoisomerases beyond the standard role. Transcription 2015; 4:232-7. [PMID: 24135702 DOI: 10.4161/trns.26598] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Chromatin is dynamically changing its structure to accommodate and control DNA-dependent processes inside of eukaryotic cells. These changes are necessarily linked to changes of DNA topology, which might itself serve as a regulatory signal to be detected by proteins. Thus, DNA Topoisomerases may contribute to the regulation of many events occurring during the transcription cycle. In this review we will focus on DNA Topoisomerase functions in transcription, with particular emphasis on the multiplicity of tasks beyond their widely appreciated role in solving topological problems associated with transcription elongation.
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177
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Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. Principles of regulatory information conservation between mouse and human. Nature 2015; 515:371-375. [PMID: 25409826 PMCID: PMC4343047 DOI: 10.1038/nature13985] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 10/21/2014] [Indexed: 11/09/2022]
Abstract
To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human-mouse erythroid progenitor, lymphoblast and embryonic stem-cell lines. By combining the genome-wide transcription factor occupancy repertoires, associated epigenetic signals, and co-association patterns, here we deduce several evolutionary principles of gene regulatory features operating since the mouse and human lineages diverged. The genomic distribution profiles, primary binding motifs, chromatin states, and DNA methylation preferences are well conserved for TF-occupied sequences. However, the extent to which orthologous DNA segments are bound by orthologous TFs varies both among TFs and with genomic location: binding at promoters is more highly conserved than binding at distal elements. Notably, occupancy-conserved TF-occupied sequences tend to be pleiotropic; they function in several tissues and also co-associate with many TFs. Single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences.
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Affiliation(s)
- Yong Cheng
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Bong-Hyun Kim
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Weisheng Wu
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Philip Cayting
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alan P Boyle
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Vasavi Sundaram
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Xiaoyun Xing
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Nergiz Dogan
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jingjing Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ghia Euskirchen
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Shin Lin
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94304, USA
| | - Yiing Lin
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA 94701,USA.,Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.,School of Natural Sciences, University of California, Merced, CA 95343,USA
| | - Trupti Kawli
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Xinqiong Yang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Dorrelyn Patacsil
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Cheryl A Keller
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda Giardine
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Len A Pennacchio
- Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA 94701,USA.,Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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178
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Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. ACTA ACUST UNITED AC 2015; 109:21.29.1-21.29.9. [PMID: 25559105 DOI: 10.1002/0471142727.mb2129s109] [Citation(s) in RCA: 1819] [Impact Index Per Article: 202.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This unit describes Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq), a method for mapping chromatin accessibility genome-wide. This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription-factor binding and nucleosome position. The method is a fast and sensitive alternative to DNase-seq for assaying chromatin accessibility genome-wide, or to MNase-seq for assaying nucleosome positions in accessible regions of the genome.
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Affiliation(s)
- Jason D Buenrostro
- Department of Genetics, Stanford University School of Medicine, Stanford, California.,Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California
| | - Beijing Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Howard Y Chang
- Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, California
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179
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Tsompana M, Buck MJ. Chromatin accessibility: a window into the genome. Epigenetics Chromatin 2014; 7:33. [PMID: 25473421 PMCID: PMC4253006 DOI: 10.1186/1756-8935-7-33] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/05/2014] [Indexed: 01/09/2023] Open
Abstract
Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to transcription factor binding. Regulatory DNA thus coincides with open or accessible genomic sites of remodeled chromatin. Current chromatin accessibility assays are used to separate the genome by enzymatic or chemical means and isolate either the accessible or protected locations. The isolated DNA is then quantified using a next-generation sequencing platform. Wide application of these assays has recently focused on the identification of the instrumental epigenetic changes responsible for differential gene expression, cell proliferation, functional diversification and disease development. Here we discuss the limitations and advantages of current genome-wide chromatin accessibility assays with especial attention on experimental precautions and sequence data analysis. We conclude with our perspective on future improvements necessary for moving the field of chromatin profiling forward.
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Affiliation(s)
- Maria Tsompana
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 USA
| | - Michael J Buck
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 USA ; Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY USA
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180
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Yardımcı GG, Frank CL, Crawford GE, Ohler U. Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. Nucleic Acids Res 2014; 42:11865-78. [PMID: 25294828 PMCID: PMC4231734 DOI: 10.1093/nar/gku810] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/22/2014] [Accepted: 08/27/2014] [Indexed: 12/31/2022] Open
Abstract
DNaseI footprinting is an established assay for identifying transcription factor (TF)-DNA interactions with single base pair resolution. High-throughput DNase-seq assays have recently been used to detect in vivo DNase footprints across the genome. Multiple computational approaches have been developed to identify DNase-seq footprints as predictors of TF binding. However, recent studies have pointed to a substantial cleavage bias of DNase and its negative impact on predictive performance of footprinting. To assess the potential for using DNase-seq to identify individual binding sites, we performed DNase-seq on deproteinized genomic DNA and determined sequence cleavage bias. This allowed us to build bias corrected and TF-specific footprint models. The predictive performance of these models demonstrated that predicted footprints corresponded to high-confidence TF-DNA interactions. DNase-seq footprints were absent under a fraction of ChIP-seq peaks, which we show to be indicative of weaker binding, indirect TF-DNA interactions or possible ChIP artifacts. The modeling approach was also able to detect variation in the consensus motifs that TFs bind to. Finally, cell type specific footprints were detected within DNase hypersensitive sites that are present in multiple cell types, further supporting that footprints can identify changes in TF binding that are not detectable using other strategies.
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Affiliation(s)
- Galip Gürkan Yardımcı
- Computational Biology and Bioinformatics Program, Duke University, Durham, NC 27708, USA Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Christopher L Frank
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Uwe Ohler
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA Max Delbruck Center for Molecular Medicine, 13125 Berlin, Germany
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181
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Banerjee AR, Kim YJ, Kim TH. A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. Nucleic Acids Res 2014; 42:12537-54. [PMID: 25348400 PMCID: PMC4227751 DOI: 10.1093/nar/gku1018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Long-range enhancers of transcription are a key component of the genomic regulatory architecture. Recent studies have identified bi-directionally transcribed RNAs emanating from these enhancers known as eRNAs. However, it remains unclear how tightly coupled eRNA production is with enhancer activity. Through our systematic search for long-range elements that interact with the interferon-β gene, a model system for studying inducible transcription, we have identified a novel enhancer, which we have named L2 that regulates the expression of interferon-β. We have demonstrated its virus-inducible enhancer activity by analyzing epigenomic profiles, transcription factor association, nascent RNA production and activity in reporter assays. This enhancer exhibits intimately linked virus-inducible enhancer and bidirectional promoter activity that is largely dependent on a conserved Interferon Stimulated Response Element and robustly generates virus inducible eRNAs. Notably, its enhancer and promoter activities are fully retained in reporter assays even upon a complete elimination of its associated eRNA sequences. Finally, we show that L2 regulates IFNB1 expression by siRNA knockdown of eRNAs, and the deletion of L2 in a BAC transfection assay. Thus, L2 is a novel enhancer that regulates IFNB1 and whose eRNAs exert significant activity in vivo that is distinct from those activities recapitulated in the luciferase reporter assays.
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Affiliation(s)
- A Raja Banerjee
- Department of Genetics, Yale University, School of Medicine, New Haven, CT 06520, USA
| | - Yoon Jung Kim
- Department of Genetics, Yale University, School of Medicine, New Haven, CT 06520, USA
| | - Tae Hoon Kim
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
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182
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Li Q, Stram A, Chen C, Kar S, Gayther S, Pharoah P, Haiman C, Stranger B, Kraft P, Freedman ML. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types. Hum Mol Genet 2014; 23:5294-302. [PMID: 24907074 PMCID: PMC4215106 DOI: 10.1093/hmg/ddu228] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/17/2014] [Accepted: 05/06/2014] [Indexed: 11/13/2022] Open
Abstract
The majority of trait-associated loci discovered through genome-wide association studies are located outside of known protein coding regions. Consequently, it is difficult to ascertain the mechanism underlying these variants and to pinpoint the causal alleles. Expression quantitative trait loci (eQTLs) provide an organizing principle to address both of these issues. eQTLs are genetic loci that correlate with RNA transcript levels. Large-scale data sets such as the Cancer Genome Atlas (TCGA) provide an ideal opportunity to systematically evaluate eQTLs as they have generated multiple data types on hundreds of samples. We evaluated the determinants of gene expression (germline variants and somatic copy number and methylation) and performed cis-eQTL analyses for mRNA expression and miRNA expression in five tumor types (breast, colon, kidney, lung and prostate). We next tested 149 known cancer risk loci for eQTL effects, and observed that 42 (28.2%) were significantly associated with at least one transcript. Lastly, we described a fine-mapping strategy for these 42 eQTL target-gene associations based on an integrated strategy that combines the eQTL level of significance and the regulatory potential as measured by DNaseI hypersensitivity. For each of the risk loci, our analyses suggested 1 to 81 candidate causal variants that may be prioritized for downstream functional analysis. In summary, our study provided a comprehensive landscape of the genetic determinants of gene expression in different tumor types and ranked the genes and loci for further functional assessment of known cancer risk loci.
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Affiliation(s)
- Qiyuan Li
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA, USA Medical College of Xiamen University, Xiamen, China Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA, USA
| | | | - Constance Chen
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Siddhartha Kar
- Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | - Simon Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Log Angeles, CA, USA
| | - Paul Pharoah
- Strangeways Research Laboratory, University of Cambridge, Cambridge, UK
| | | | - Barbara Stranger
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA, USA Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA, USA
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183
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Abstract
Enhancers are selectively utilized to orchestrate gene expression programs that first govern pluripotency and then proceed to highly specialized programs required for the process of cellular differentiation. Whereas gene-proximal promoters are typically active across numerous cell types, distal enhancer activation is cell-type-specific and central to cell fate determination, thereby accounting for cell identity. Recent studies have highlighted the diversity of enhancer usage, cataloguing millions of such elements in the human genome. The disruption of enhancer activity, through genetic or epigenetic alterations, can impact cell-type-specific functions, resulting in a wide range of pathologies. In cancer, these alterations can promote a 'cell identity crisis', in which enhancers associated with oncogenes and multipotentiality are activated, while those promoting cell fate commitment are inactivated. Overall, these alterations favor an undifferentiated cellular phenotype. Here, we review the current knowledge regarding the role of enhancers in normal cell function, and discuss how genetic and epigenetic changes in enhancer elements potentiate oncogenesis. In addition, we discuss how understanding the mechanisms regulating enhancer activity can inform therapeutic opportunities in cancer cells and highlight key challenges that remain in understanding enhancer biology as it relates to oncology.
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Affiliation(s)
- Ken J Kron
- The Princess Margaret Cancer Centre - University Health Network, Toronto, ON M5G 1 L7 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Swneke D Bailey
- The Princess Margaret Cancer Centre - University Health Network, Toronto, ON M5G 1 L7 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1 L7 Canada
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre - University Health Network, Toronto, ON M5G 1 L7 Canada ; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1 L7 Canada ; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3 Canada
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184
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Prediction of DNase I hypersensitive sites by using pseudo nucleotide compositions. ScientificWorldJournal 2014; 2014:740506. [PMID: 25215331 PMCID: PMC4152949 DOI: 10.1155/2014/740506] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 08/03/2014] [Indexed: 11/19/2022] Open
Abstract
DNase I hypersensitive sites (DHS) associated with a wide variety of regulatory DNA elements. Knowledge about the locations of DHS is helpful for deciphering the function of noncoding genomic regions. With the acceleration of genome sequences in the postgenomic age, it is highly desired to develop cost-effective computational methods to identify DHS. In the present work, a support vector machine based model was proposed to identify DHS by using the pseudo dinucleotide composition. In the jackknife test, the proposed model obtained an accuracy of 83%, which is competitive with that of the existing method. This result suggests that the proposed model may become a useful tool for DHS identifications.
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185
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Inoue K, Imai Y. Identification of novel transcription factors in osteoclast differentiation using genome-wide analysis of open chromatin determined by DNase-seq. J Bone Miner Res 2014; 29:1823-32. [PMID: 24677342 DOI: 10.1002/jbmr.2229] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/10/2014] [Accepted: 03/14/2014] [Indexed: 12/11/2022]
Abstract
Clarification of the mechanisms underlying osteoclast differentiation enables us to understand the physiology of bone metabolism as well as the pathophysiology of bone diseases such as osteoporosis. Recently, it has been reported that epigenetics can determine cell fate and regulate cell type-specific gene expression. However, little is known about epigenetics during osteoclastogenesis. To reveal a part of epigenetics, especially focused on chromatin dynamics, during early osteoclastogenesis and to identify novel transcription factors involved in osteoclastogenesis, we performed a genome-wide analysis of open chromatin during receptor activator of NF-κB ligand (RANKL)-induced osteoclastogenesis using DNase I hypersensitive sites sequencing (DNase-seq). DNase-seq was performed using the extracted nuclei from RAW264 cells treated with or without RANKL for 24 hours, followed by several bioinformatic analyses. DNase I hypersensitive sites (DHSs) were dynamically changed during RANKL-induced osteoclastogenesis and they accumulated in promoter regions. The distributions of DHSs among cis-regulatory DNA regions were identical regardless of RANKL stimulation. Motif discovery analysis successfully identified well-known osteoclastogenic transcription factors including Jun, CREB1, FOS, ATF2, and ATF4, but also novel transcription factors for osteoclastogenesis such as Zscan10, Atf1, Nrf1, and Srebf2. siRNA knockdown of these identified novel transcription factors impaired osteoclastogenesis. Taken together, DNase-seq is a useful tool for comprehension of epigenetics, especially chromatin dynamics during osteoclastogenesis and for identification of novel transcription factors involved in osteoclastogenesis. This study may reveal underlying mechanisms that determine cell type-specific differentiation of bone cells and may lead to investigation of novel therapeutic targets for osteoporosis.
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Affiliation(s)
- Kazuki Inoue
- Division of Integrative Pathophysiology, Proteo-Science Center, Graduate School of Medicine, Ehime University, Ehime, Japan; Department of Biological Resources, Integrated Center for Sciences, Ehime University, Ehime, Japan
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186
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Kamath U, De Jong K, Shehu A. Effective automated feature construction and selection for classification of biological sequences. PLoS One 2014; 9:e99982. [PMID: 25033270 PMCID: PMC4102475 DOI: 10.1371/journal.pone.0099982] [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: 09/12/2013] [Accepted: 05/21/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Many open problems in bioinformatics involve elucidating underlying functional signals in biological sequences. DNA sequences, in particular, are characterized by rich architectures in which functional signals are increasingly found to combine local and distal interactions at the nucleotide level. Problems of interest include detection of regulatory regions, splice sites, exons, hypersensitive sites, and more. These problems naturally lend themselves to formulation as classification problems in machine learning. When classification is based on features extracted from the sequences under investigation, success is critically dependent on the chosen set of features. METHODOLOGY We present an algorithmic framework (EFFECT) for automated detection of functional signals in biological sequences. We focus here on classification problems involving DNA sequences which state-of-the-art work in machine learning shows to be challenging and involve complex combinations of local and distal features. EFFECT uses a two-stage process to first construct a set of candidate sequence-based features and then select a most effective subset for the classification task at hand. Both stages make heavy use of evolutionary algorithms to efficiently guide the search towards informative features capable of discriminating between sequences that contain a particular functional signal and those that do not. RESULTS To demonstrate its generality, EFFECT is applied to three separate problems of importance in DNA research: the recognition of hypersensitive sites, splice sites, and ALU sites. Comparisons with state-of-the-art algorithms show that the framework is both general and powerful. In addition, a detailed analysis of the constructed features shows that they contain valuable biological information about DNA architecture, allowing biologists and other researchers to directly inspect the features and potentially use the insights obtained to assist wet-laboratory studies on retainment or modification of a specific signal. Code, documentation, and all data for the applications presented here are provided for the community at http://www.cs.gmu.edu/~ashehu/?q=OurTools.
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Affiliation(s)
- Uday Kamath
- Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Kenneth De Jong
- Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Krasnow Institute, George Mason University, Fairfax, Virginia, United States of America
| | - Amarda Shehu
- Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Bioengineering, George Mason University, Fairfax, Virginia, United States of America
- School of Systems Biology, George Mason University, Fairfax, Virginia, United States of America
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187
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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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188
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Zhang W, Zhang T, Wu Y, Jiang J. Open Chromatin in Plant Genomes. Cytogenet Genome Res 2014; 143:18-27. [DOI: 10.1159/000362827] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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189
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Kapoor A, Sekar R, Hansen N, Fox-Talbot K, Morley M, Pihur V, Chatterjee S, Brandimarto J, Moravec C, Pulit S, Pfeufer A, Mullikin J, Ross M, Green E, Bentley D, Newton-Cheh C, Boerwinkle E, Tomaselli G, Cappola T, Arking D, Halushka M, Chakravarti A, Chakravarti A. An enhancer polymorphism at the cardiomyocyte intercalated disc protein NOS1AP locus is a major regulator of the QT interval. Am J Hum Genet 2014; 94:854-69. [PMID: 24857694 DOI: 10.1016/j.ajhg.2014.05.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/01/2014] [Indexed: 11/27/2022] Open
Abstract
QT interval variation is assumed to arise from variation in repolarization as evidenced from rare Na- and K-channel mutations in Mendelian QT prolongation syndromes. However, in the general population, common noncoding variants at a chromosome 1q locus are the most common genetic regulators of QT interval variation. In this study, we use multiple human genetic, molecular genetic, and cellular assays to identify a functional variant underlying trait association: a noncoding polymorphism (rs7539120) that maps within an enhancer of NOS1AP and affects cardiac function by increasing NOS1AP transcript expression. We further localized NOS1AP to cardiomyocyte intercalated discs (IDs) and demonstrate that overexpression of NOS1AP in cardiomyocytes leads to altered cellular electrophysiology. We advance the hypothesis that NOS1AP affects cardiac electrical conductance and coupling and thereby regulates the QT interval through propagation defects. As further evidence of an important role for propagation variation affecting QT interval in humans, we show that common polymorphisms mapping near a specific set of 170 genes encoding ID proteins are significantly enriched for association with the QT interval, as compared to genome-wide markers. These results suggest that focused studies of proteins within the cardiomyocyte ID are likely to provide insights into QT prolongation and its associated disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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190
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Luo Y, Rao M, Zou J. Generation of GFP Reporter Human Induced Pluripotent Stem Cells Using AAVS1 Safe Harbor Transcription Activator-Like Effector Nuclease. ACTA ACUST UNITED AC 2014; 29:5A.7.1-18. [PMID: 24838915 DOI: 10.1002/9780470151808.sc05a07s29] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Generation of a fluorescent GFP reporter line in human induced pluripotent stem cells (hiPSCs) provides enormous potentials in both basic stem cell research and regenerative medicine. A protocol for efficiently generating such an engineered reporter line by gene targeting is highly desired. Transcription activator-like effector nucleases (TALENs) are a new class of artificial restriction enzymes that have been shown to significantly promote homologous recombination by >1000-fold. The AAVS1 (adeno-associated virus integration site 1) locus is a "safe harbor" and has an open chromatin structure that allows insertion and stable expression of transgene. Here, we describe a step-by-step protocol from determination of TALENs activity, hiPSC culture, and delivery of a donor into AAVS1 targeting site, to validation of targeted integration by PCR and Southern blot analysis using hiPSC line, and a pair of open-source AAVS1 TALENs.
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Affiliation(s)
- Yongquan Luo
- NIH Center for Regenerative Medicine, Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Medicine, Bethesda, Maryland
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191
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Cadiz-Rivera B, Fromm G, de Vries C, Fields J, McGrath KE, Fiering S, Bulger M. The chromatin "landscape" of a murine adult β-globin gene is unaffected by deletion of either the gene promoter or a downstream enhancer. PLoS One 2014; 9:e92947. [PMID: 24817273 PMCID: PMC4015891 DOI: 10.1371/journal.pone.0092947] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 02/27/2014] [Indexed: 01/11/2023] Open
Abstract
In mammals, the complex tissue- and developmental-specific expression of genes within the β-globin cluster is known to be subject to control by the gene promoters, by a locus control region (LCR) located upstream of the cluster, and by sequence elements located across the intergenic regions. Despite extensive investigation, however, the complement of sequences that is required for normal regulation of chromatin structure and gene expression within the cluster is not fully defined. To further elucidate regulation of the adult β-globin genes, we investigate the effects of two deletions engineered within the endogenous murine β-globin locus. First, we find that deletion of the β2-globin gene promoter, while eliminating β2-globin gene expression, results in no additional effects on chromatin structure or gene expression within the cluster. Notably, our observations are not consistent with competition among the β-globin genes for LCR activity. Second, we characterize a novel enhancer located 3′ of the β2-globin gene, but find that deletion of this sequence has no effect whatsoever on gene expression or chromatin structure. This observation highlights the difficulty in assigning function to enhancer sequences identified by the chromatin “landscape” or even by functional assays.
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Affiliation(s)
- Brenda Cadiz-Rivera
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
| | - George Fromm
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
- National Institute for Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, United States of America
| | - Christina de Vries
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
| | - Jennifer Fields
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Kathleen E. McGrath
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
| | - Steven Fiering
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire, United States of America
| | - Michael Bulger
- Department of Pediatrics, University of Rochester Medical Center and Center for Pediatric Biomedical Research, Rochester, New York, United States of America
- * E-mail:
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192
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Abstract
With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease.
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193
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Dimitrova A, Ananiev E, Gecheff K. Dnase I Hypersensitive Sites within the Intergenic Spacer of Ribosomal RNA Genes in Reconstructed Barley Karyotypes. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10817608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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194
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Zhang H, Gao L, Anandhakumar J, Gross DS. Uncoupling transcription from covalent histone modification. PLoS Genet 2014; 10:e1004202. [PMID: 24722509 PMCID: PMC3983032 DOI: 10.1371/journal.pgen.1004202] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/08/2014] [Indexed: 12/04/2022] Open
Abstract
It is widely accepted that transcriptional regulation of eukaryotic genes is intimately coupled to covalent modifications of the underlying chromatin template, and in certain cases the functional consequences of these modifications have been characterized. Here we present evidence that gene activation in the silent heterochromatin of the yeast Saccharomyces cerevisiae can occur in the context of little, if any, covalent histone modification. Using a SIR-regulated heat shock-inducible transgene, hsp82-2001, and a natural drug-inducible subtelomeric gene, YFR057w, as models we demonstrate that substantial transcriptional induction (>200-fold) can occur in the context of restricted histone loss and negligible levels of H3K4 trimethylation, H3K36 trimethylation and H3K79 dimethylation, modifications commonly linked to transcription initiation and elongation. Heterochromatic gene activation can also occur with minimal H3 and H4 lysine acetylation and without replacement of H2A with the transcription-linked variant H2A.Z. Importantly, absence of histone modification does not stem from reduced transcriptional output, since hsp82-ΔTATA, a euchromatic promoter mutant lacking a TATA box and with threefold lower induced transcription than heterochromatic hsp82-2001, is strongly hyperacetylated in response to heat shock. Consistent with negligible H3K79 dimethylation, dot1Δ cells lacking H3K79 methylase activity show unimpeded occupancy of RNA polymerase II within activated heterochromatic promoter and coding regions. Our results indicate that large increases in transcription can be observed in the virtual absence of histone modifications often thought necessary for gene activation. The proper regulation of gene expression is of fundamental importance in the maintenance of normal growth and development. Misregulation of genes can lead to such outcomes as cancer, diabetes and neurodegenerative disease. A key step in gene regulation occurs during the transcription of the chromosomal DNA into messenger RNA by the enzyme, RNA polymerase II. Histones are small, positively charged proteins that package genomic DNA into arrays of bead-like particles termed nucleosomes, the principal components of chromatin. Increasing evidence suggests that nucleosomal histones play an active role in regulating transcription, and that this is derived in part from reversible chemical (“covalent”) modifications that take place on their amino acids. These histone modifications create novel surfaces on nucleosomes that can serve as docking sites for other proteins that control a gene's expression state. In this study we present evidence that contrary to the general case, covalent modifications typically associated with transcription are minimally used by genes embedded in a specialized, condensed chromatin structure termed heterochromatin in the model organism baker's yeast. Our observations are significant, for they suggest that gene transcription can occur in a living cell in the virtual absence of covalent modification of the chromatin template.
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Affiliation(s)
- Hesheng Zhang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Lu Gao
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - Jayamani Anandhakumar
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | - David S. Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
- * E-mail:
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195
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Austin JW, Lu P, Majumder P, Ahmed R, Boss JM. STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells. THE JOURNAL OF IMMUNOLOGY 2014; 192:4876-86. [PMID: 24711622 DOI: 10.4049/jimmunol.1302750] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Programmed death-1 (PD-1) is a crucial negative regulator of CD8 T cell development and function, yet the mechanisms that control its expression are not fully understood. Through a nonbiased DNase I hypersensitivity assay, four novel regulatory regions within the Pdcd1 locus were identified. Two of these elements flanked the locus, bound the transcriptional insulator protein CCCTC-binding factor, and interacted with each other, creating a potential regulatory compartmentalization of the locus. In response to T cell activation signaling, NFATc1 bound to two of the novel regions that function as independent regulatory elements. STAT binding sites were identified in these elements as well. In splenic CD8 T cells, TCR-induced PD-1 expression was augmented by IL-6 and IL-12, inducers of STAT3 and STAT4 activity, respectively. IL-6 or IL-12 on its own did not induce PD-1. Importantly, STAT3/4 and distinct chromatin modifications were associated with the novel regulatory regions following cytokine stimulation. The NFATc1/STAT regulatory regions were found to interact with the promoter region of the Pdcd1 gene, providing a mechanism for their action. Together these data add multiple novel distal regulatory regions and pathways to the control of PD-1 expression and provide a molecular mechanism by which proinflammatory cytokines, such as IL-6 or IL-12, can augment PD-1 expression.
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196
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Lam MTY, Li W, Rosenfeld MG, Glass CK. Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci 2014; 39:170-82. [PMID: 24674738 DOI: 10.1016/j.tibs.2014.02.007] [Citation(s) in RCA: 371] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/20/2014] [Accepted: 02/20/2014] [Indexed: 01/06/2023]
Abstract
A large portion of the human genome is transcribed into RNAs without known protein-coding functions, far outnumbering coding transcription units. Extensive studies of long noncoding RNAs (lncRNAs) have clearly demonstrated that they can play critical roles in regulating gene expression, development, and diseases, acting both as transcriptional activators and repressors. More recently, enhancers have been found to be broadly transcribed, resulting in the production of enhancer-derived RNAs, or eRNAs. Here, we review emerging evidence suggesting that at least some eRNAs contribute to enhancer function. We discuss these findings with respect to potential mechanisms of action of eRNAs and other ncRNAs in regulated gene expression.
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Affiliation(s)
- Michael T Y Lam
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Wenbo Li
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA; Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
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197
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Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN. The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. BMC Genomics 2014; 15:92. [PMID: 24484546 PMCID: PMC3928079 DOI: 10.1186/1471-2164-15-92] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 01/30/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins. RESULTS Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1 in Drosophila S2 cells. Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks. We find that the ratio of HMGD1 to H1 binding is a better predictor of gene activity than either protein by itself, which suggests that reciprocal binding between these proteins is important for gene regulation. Using knockdown experiments, we show that HMGD1 and H1 affect the occupancy of the other protein, change nucleosome repeat length and modulate gene expression. CONCLUSION Collectively, our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and their linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. This study provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation.
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198
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Rapid and unambiguous detection of DNase I hypersensitive site in rare population of cells. PLoS One 2014; 9:e85740. [PMID: 24465674 PMCID: PMC3897510 DOI: 10.1371/journal.pone.0085740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 12/02/2013] [Indexed: 11/19/2022] Open
Abstract
DNase I hypersensitive (DHS) sites are important for understanding cis regulation of gene expression. However, existing methods for detecting DHS sites in small numbers of cells can lead to ambiguous results. Here we describe a simple new method, in which DNA fragments with ends generated by DNase I digestion are isolated and used as templates for two PCR reactions. In the first PCR, primers are derived from sequences up- and down-stream of the DHS site. If the DHS site exists in the cells, the first PCR will not produce PCR products due to the cuts of the templates by DNase I between the primer sequences. In the second PCR, one primer is derived from sequence outside the DHS site and the other from the adaptor. This will produce a smear of PCR products of different sizes due to cuts by DNase I at different positions at the DHS site. With this design, we detected a DHS site at the CD4 gene in two CD4 T cell populations using as few as 2×10(4) cells. We further validated this method by detecting a DHS site of the IL-4 gene that is specifically present in type 2 but not type 1 T helper cells. Overall, this method overcomes the interference by genomic DNA not cut by DNase I at the DHS site, thereby offering unambiguous detection of DHS sites in the cells.
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199
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John S, Sabo PJ, Canfield TK, Lee K, Vong S, Weaver M, Wang H, Vierstra J, Reynolds AP, Thurman RE, Stamatoyannopoulos JA. Genome-scale mapping of DNase I hypersensitivity. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2014; Chapter 27:Unit 21.27. [PMID: 23821440 DOI: 10.1002/0471142727.mb2127s103] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
DNase I-seq is a global and high-resolution method that uses the nonspecific endonuclease DNase I to map chromatin accessibility. These accessible regions, designated as DNase I hypersensitive sites (DHSs), define the regulatory features, (e.g., promoters, enhancers, insulators, and locus control regions) of complex genomes. In this unit, methods are described for nuclei isolation, digestion of nuclei with limiting concentrations of DNase I, and the biochemical fractionation of DNase I hypersensitive sites in preparation for high-throughput sequencing. DNase I-seq is an unbiased and robust method that is not predicated on an a priori understanding of regulatory patterns or chromatin features.
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Affiliation(s)
- Sam John
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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200
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Webster DE, Barajas B, Bussat RT, Yan KJ, Neela PH, Flockhart RJ, Kovalski J, Zehnder A, Khavari PA. Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition. Genome Res 2014; 24:751-60. [PMID: 24443471 PMCID: PMC4009605 DOI: 10.1101/gr.166231.113] [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] [Indexed: 11/25/2022]
Abstract
Thousands of putative enhancers are characterized in the human genome, yet few have been shown to have a functional role in cancer progression. Inhibiting oncokinases, such as EGFR, ALK, ERBB2, and BRAF, is a mainstay of current cancer therapy but is hindered by innate drug resistance mediated by up-regulation of the HGF receptor, MET. The mechanisms mediating such genomic responses to targeted therapy are unknown. Here, we identify lineage-specific enhancers at the MET locus for multiple common tumor types, including a melanoma lineage-specific enhancer 63 kb downstream from the MET TSS. This enhancer displays inducible chromatin looping with the MET promoter to up-regulate MET expression upon BRAF inhibition. Epigenomic analysis demonstrated that the melanocyte-specific transcription factor, MITF, mediates this enhancer function. Targeted genomic deletion (<7 bp) of the MITF motif within the MET enhancer suppressed inducible chromatin looping and innate drug resistance, while maintaining MITF-dependent, inhibitor-induced melanoma cell differentiation. Epigenomic analysis can thus guide functional disruption of regulatory DNA to decouple pro- and anti-oncogenic functions of a dominant transcription factor and block innate resistance to oncokinase therapy.
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Affiliation(s)
- Dan E Webster
- The Veterans Affairs Palo Alto Healthcare System, Palo Alto, California 94304, USA; The Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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