201
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Glass CK. Genetic and genomic approaches to understanding macrophage identity and function. Arterioscler Thromb Vasc Biol 2015; 35:755-62. [PMID: 25745059 DOI: 10.1161/atvbaha.114.304051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A major goal of our laboratory is to understand the molecular mechanisms that underlie the development and functions of diverse macrophage phenotypes in health and disease. Recent studies using genetic and genomic approaches suggest a relatively simple model of collaborative and hierarchical interactions between lineage-determining and signal-dependent transcription factors that enable selection and activation of transcriptional enhancers that specify macrophage identity and function. In addition, we have found that it is possible to use natural genetic variation as a powerful tool for advancing our understanding of how the macrophage deciphers the information encoded by the genome to attain specific phenotypes in a context-dependent manner. Here, I will describe our recent efforts to extend genetic and genomic approaches to investigate the roles of distinct tissue environments in determining the phenotypes of different resident populations of macrophages.
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Affiliation(s)
- Christopher K Glass
- From the Department of Cellular and Molecular Medicine, University of California, San Diego.
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202
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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: 32] [Impact Index Per Article: 3.6] [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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203
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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: 1507] [Impact Index Per Article: 167.4] [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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204
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Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A. Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens. Science 2015; 347:1259038. [PMID: 25745177 DOI: 10.1126/science.1259038] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein expression is regulated by the production and degradation of messenger RNAs (mRNAs) and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics so as to build a quantitative genomic model of the differential regulation of gene expression in lipopolysaccharide-stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for more than half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction for newly activated cellular functions and by protein life-cycle changes for remodeling of preexisting functions.
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Affiliation(s)
- Marko Jovanovic
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Rooney
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Philipp Mertins
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Nicolas Chevrier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Harvard Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rahul Satija
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Edwin H Rodriguez
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alexander P Fields
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Schraga Schwartz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Thomas Eisenhaure
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michal Rabani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dave Gennert
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Diana Lu
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Toni Delorey
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA. Howard Hughes Medical Institute (HHMI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nir Hacohen
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA. Harvard Medical School, Boston, MA 02115, USA.
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA. HHMI, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
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205
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Jurida L, Soelch J, Bartkuhn M, Handschick K, Müller H, Newel D, Weber A, Dittrich-Breiholz O, Schneider H, Bhuju S, Saul VV, Schmitz ML, Kracht M. The Activation of IL-1-Induced Enhancers Depends on TAK1 Kinase Activity and NF-κB p65. Cell Rep 2015; 10:726-739. [PMID: 25660023 DOI: 10.1016/j.celrep.2015.01.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/13/2014] [Accepted: 12/26/2014] [Indexed: 01/02/2023] Open
Abstract
The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the genome-wide binding of the TAK1-controlled NF-κB subunit p65 in relation to active enhancers and promoters of transcribed genes by chromatin immunoprecipitation sequencing (ChIP-seq) experiments. Out of 35,000 active enhancer regions, 410 H3K4me1-positive enhancers show interleukin 1 (IL-1)-induced H3K27ac and p65 binding. Inhibition of TAK1 or IKK2 or depletion of p65 blocked inducible enhancer activation and gene expression. As exemplified by the CXC chemokine cluster located on chromosome 4, the TAK1-p65 pathway also regulates the recruitment kinetics of the histone acetyltransferase CBP, of NF-κB p50, and of AP-1 transcription factors to both promoters and enhancers. This study provides a high-resolution view of epigenetic changes occurring during the IL-1 response and allows the genome-wide identification of a distinct class of inducible p65 NF-κB-dependent enhancers in epithelial cells.
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Affiliation(s)
- Liane Jurida
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Johanna Soelch
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Katja Handschick
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Helmut Müller
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Doris Newel
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Axel Weber
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | | | - Heike Schneider
- Institute of Physiological Chemistry, Medical School Hannover, 30625 Hannover, Germany
| | - Sabin Bhuju
- Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Vera V Saul
- Institute of Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
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206
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Schönheit J, Leutz A, Rosenbauer F. Chromatin Dynamics during Differentiation of Myeloid Cells. J Mol Biol 2015; 427:670-87. [DOI: 10.1016/j.jmb.2014.08.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/05/2014] [Accepted: 08/20/2014] [Indexed: 12/23/2022]
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207
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Saccani S, Trabucchi M. Regulation of stimulus-inducible gene expression in myeloid cells. Semin Immunol 2015; 27:33-43. [DOI: 10.1016/j.smim.2015.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 02/14/2015] [Accepted: 02/19/2015] [Indexed: 12/16/2022]
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208
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Mancino A, Termanini A, Barozzi I, Ghisletti S, Ostuni R, Prosperini E, Ozato K, Natoli G. A dual cis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages. Genes Dev 2015; 29:394-408. [PMID: 25637355 PMCID: PMC4335295 DOI: 10.1101/gad.257592.114] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The transcription factor IRF8 controls both developmental and inflammatory stimulus-inducible genes in macrophages. Mancino et al. found that IRF8 is recruited to distinct sets of DNA consensus sequences before and after lipopolysaccharide (LPS) stimulation. While constitutively expressed IRF8-dependent genes contained only sites mediating basal IRF8/PU.1 recruitment, inducible IRF8-dependent genes contained variable combinations of constitutive and inducible sites. The transcription factor (TF) interferon regulatory factor 8 (IRF8) controls both developmental and inflammatory stimulus-inducible genes in macrophages, but the mechanisms underlying these two different functions are largely unknown. One possibility is that these different roles are linked to the ability of IRF8 to bind alternative DNA sequences. We found that IRF8 is recruited to distinct sets of DNA consensus sequences before and after lipopolysaccharide (LPS) stimulation. In resting cells, IRF8 was mainly bound to composite sites together with the master regulator of myeloid development PU.1. Basal IRF8–PU.1 binding maintained the expression of a broad panel of genes essential for macrophage functions (such as microbial recognition and response to purines) and contributed to basal expression of many LPS-inducible genes. After LPS stimulation, increased expression of IRF8, other IRFs, and AP-1 family TFs enabled IRF8 binding to thousands of additional regions containing low-affinity multimerized IRF sites and composite IRF–AP-1 sites, which were not premarked by PU.1 and did not contribute to the basal IRF8 cistrome. While constitutively expressed IRF8-dependent genes contained only sites mediating basal IRF8/PU.1 recruitment, inducible IRF8-dependent genes contained variable combinations of constitutive and inducible sites. Overall, these data show at the genome scale how the same TF can be linked to constitutive and inducible gene regulation via distinct combinations of alternative DNA-binding sites.
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Affiliation(s)
- Alessandra Mancino
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Alberto Termanini
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Renato Ostuni
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Keiko Ozato
- Laboratory of Molecular Growth Regulation, Genomics of Differentiation Program, National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy;
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209
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Subramanian N, Torabi-Parizi P, Gottschalk RA, Germain RN, Dutta B. Network representations of immune system complexity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:13-38. [PMID: 25625853 PMCID: PMC4339634 DOI: 10.1002/wsbm.1288] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 12/25/2022]
Abstract
The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host defense. These networks range from those involving gene regulatory and protein–protein interactions underlying intracellular signaling pathways and single‐cell responses to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism. Immunity is thus not the product of simple signaling events but rather nonlinear behaviors arising from dynamic, feedback‐regulated interactions among many components. One of the major goals of systems immunology is to quantitatively measure these complex multiscale spatial and temporal interactions, permitting development of computational models that can be used to predict responses to perturbation. Recent technological advances permit collection of comprehensive datasets at multiple molecular and cellular levels, while advances in network biology support representation of the relationships of components at each level as physical or functional interaction networks. The latter facilitate effective visualization of patterns and recognition of emergent properties arising from the many interactions of genes, molecules, and cells of the immune system. We illustrate the power of integrating ‘omics’ and network modeling approaches for unbiased reconstruction of signaling and transcriptional networks with a focus on applications involving the innate immune system. We further discuss future possibilities for reconstruction of increasingly complex cellular‐ and organism‐level networks and development of sophisticated computational tools for prediction of emergent immune behavior arising from the concerted action of these networks. WIREs Syst Biol Med 2015, 7:13–38. doi: 10.1002/wsbm.1288 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Macromolecular Interactions, Methods
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Affiliation(s)
- Naeha Subramanian
- Institute for Systems Biology, Seattle, WA, USA; Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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210
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Chabbert CD, Adjalley SH, Klaus B, Fritsch ES, Gupta I, Pelechano V, Steinmetz LM. A high-throughput ChIP-Seq for large-scale chromatin studies. Mol Syst Biol 2015; 11:777. [PMID: 25583149 PMCID: PMC4332152 DOI: 10.15252/msb.20145776] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We present a modified approach of chromatin immuno-precipitation followed by sequencing (ChIP-Seq), which relies on the direct ligation of molecular barcodes to chromatin fragments, thereby permitting experimental scale-up. With Bar-ChIP now enabling the concurrent profiling of multiple DNA–protein interactions, we report the simultaneous generation of 90 ChIP-Seq datasets without any robotic instrumentation. We demonstrate that application of Bar-ChIP to a panel of Saccharomyces cerevisiae chromatin-associated mutants provides a rapid and accurate genome-wide overview of their chromatin status. Additionally, we validate the utility of this technology to derive novel biological insights by identifying a role for the Rpd3S complex in maintaining H3K14 hypo-acetylation in gene bodies. We also report an association between the presence of intragenic H3K4 tri-methylation and the emergence of cryptic transcription in a Set2 mutant. Finally, we uncover a crosstalk between H3K14 acetylation and H3K4 methylation in this mutant. These results show that Bar-ChIP enables biological discovery through rapid chromatin profiling at single-nucleosome resolution for various conditions and protein modifications at once.
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Affiliation(s)
| | - Sophie H Adjalley
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Bernd Klaus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Emilie S Fritsch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Ishaan Gupta
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vicent Pelechano
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany Stanford Genome Technology Center, Palo Alto, CA, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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211
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Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 2015; 516:56-61. [PMID: 25471879 PMCID: PMC4256722 DOI: 10.1038/nature13920] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/07/2014] [Indexed: 01/15/2023]
Abstract
Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates, but the regulatory circuits specifying these states and enabling transitions between them are not well understood. We set out to characterize transcriptional heterogeneity in PSCs by single-cell expression profiling under different chemical and genetic perturbations. Signaling factors and developmental regulators show highly variable expression, with expression states for some variable genes heritable through multiple cell divisions. Expression variability and population heterogeneity can be influenced by perturbation of signaling pathways and chromatin regulators. Strikingly, either removal of mature miRNAs or pharmacologic blockage of signaling pathways drives PSCs into a low-noise ground state characterized by a reconfigured pluripotency network, enhanced self-renewal, and a distinct chromatin state, an effect mediated by opposing miRNA families acting on the c-myc / Lin28 / let-7 axis. These data illuminate the nature of transcriptional heterogeneity in PSCs.
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212
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Beyond receptors and signaling: epigenetic factors in the regulation of innate immunity. Immunol Cell Biol 2015; 93:233-44. [PMID: 25559622 PMCID: PMC4885213 DOI: 10.1038/icb.2014.101] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 10/31/2014] [Indexed: 12/14/2022]
Abstract
The interaction of innate immune cells with pathogens leads to changes in gene expression that elicit our body's first line of defense against infection. Although signaling pathways and transcription factors have a central role, it is becoming increasingly clear that epigenetic factors, in the form of DNA or histone modifications, as well as noncoding RNAs, are critical for generating the necessary cell lineage as well as context‐specific gene expression in diverse innate immune cell types. Much of the epigenetic landscape is set during cellular differentiation; however, pathogens and other environmental triggers also induce changes in histone modifications that can either promote tolerance or ‘train’ innate immune cells for a more robust antigen‐independent secondary response. Here we review the important contribution of epigenetic factors to the initiation, maintenance and training of innate immune responses. In addition, we explore how pathogens have hijacked these mechanisms for their benefit and the potential of small molecules targeting chromatin machinery as a way to boost or subdue the innate immune response in disease. The March 2015 issue contains a Special Feature on the epigenetic mechanisms underlying health and disease. Epigenetic modifications to chromatin influence the transcriptional status of our genes. Thus, understanding the epigenetic mechanisms that regulate immune cell fate are of great importance as they will provide insight into not only how to boost immune responses but also alter harmful ones such as autoimmunity and cancer. Immunology and Cell Biology thanks the coordinators of this Special Feature ‐ Rhys Allan ‐ for his planning and input.
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213
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Colleran A, Collins PE, Carmody RJ. Assessing sites of NF-κB DNA binding using chromatin immunoprecipitation. Methods Mol Biol 2015; 1280:47-59. [PMID: 25736743 DOI: 10.1007/978-1-4939-2422-6_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The NF-κB transcription factor is in fact a family of related proteins which dimerize to form at least 12 distinct complexes which regulate the expression of hundred of genes of importance to a range of physiological and pathological processes. The binding of NF-κB to the regulatory regions and promoters of target genes is influenced by a number of factors including the sequence of DNA-binding sites, the posttranslational modification of NF-κB, and the interaction of cofactors and co-regulators of transcription. In addition, the binding of NF-κB to promoters is highly dynamic and the recruitment of specific subunits to specific binding sites may occur with distinct kinetics. Moreover, genome-wide analysis of NF-κB chromatin binding indicates that the majority of DNA-binding events are not associated with changes in transcriptional activity. Thus, the analysis of NF-κB recruitment and activity at specific binding sites is of critical importance in understanding the regulation of transcription. In this chapter we describe a chromatin immunoprecipitation assay to investigate the in situ binding of NF-κB to specific sites in the genome.
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Affiliation(s)
- Amy Colleran
- Institute of Infection, Immunology and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
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214
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Joshi A. Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs. BMC Bioinformatics 2014; 15:412. [PMID: 25547756 PMCID: PMC4302108 DOI: 10.1186/s12859-014-0412-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/08/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Transcriptional hotspots are defined as genomic regions bound by multiple factors. They have been identified recently as cell type specific enhancers regulating developmentally essential genes in many species such as worm, fly and humans. The in-depth analysis of hotspots across multiple cell types in same species still remains to be explored and can bring new biological insights. RESULTS We therefore collected 108 transcription-related factor (TF) ChIP sequencing data sets in ten murine cell types and classified the peaks in each cell type in three groups according to binding occupancy as singletons (low-occupancy), combinatorials (mid-occupancy) and hotspots (high-occupancy). The peaks in the three groups clustered largely according to the occupancy, suggesting priming of genomic loci for mid occupancy irrespective of cell type. We then characterized hotspots for diverse structural functional properties. The genes neighbouring hotspots had a small overlap with hotspot genes in other cell types and were highly enriched for cell type specific function. Hotspots were enriched for sequence motifs of key TFs in that cell type and more than 90% of hotspots were occupied by pioneering factors. Though we did not find any sequence signature in the three groups, the H3K4me1 binding profile had bimodal peaks at hotspots, distinguishing hotspots from mono-modal H3K4me1 singletons. In ES cells, differentially expressed genes after perturbation of activators were enriched for hotspot genes suggesting hotspots primarily act as transcriptional activator hubs. Finally, we proposed that ES hotspots might be under control of SetDB1 and not DNMT for silencing. CONCLUSION Transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes. In ES cells, they are predicted to act as transcriptional activator hubs and might be under SetDB1 control for silencing.
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Affiliation(s)
- Anagha Joshi
- Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 8GR, UK.
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215
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Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature 2014; 518:355-359. [PMID: 25533951 PMCID: PMC4336237 DOI: 10.1038/nature13990] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 10/21/2014] [Indexed: 12/16/2022]
Abstract
Models derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signalling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells in the embryonic and adult nervous system. Here we report the transcriptional and epigenomic analysis of six consecutive neural progenitor cell stages derived from a HES5::eGFP reporter human embryonic stem cell line. Using this system, we aimed to model cell-fate decisions including specification, expansion and patterning during the ontogeny of cortical neural stem and progenitor cells. In order to dissect regulatory mechanisms that orchestrate the stage-specific differentiation process, we developed a computational framework to infer key regulators of each cell-state transition based on the progressive remodelling of the epigenetic landscape and then validated these through a pooled short hairpin RNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and suggest here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our system and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation.
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216
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Vandenbon A, Teraguchi S, Takeuchi O, Suzuki Y, Standley DM. Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation. BMC Genomics 2014; 15 Suppl 10:S4. [PMID: 25560382 PMCID: PMC4304210 DOI: 10.1186/1471-2164-15-s10-s4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies have underscored the role of enhancers in defining cell type-specific transcriptomes. Cell type-specific enhancers are bound by combinations of shared and cell type-specific transcription factors (TFs). However, little is known about combinatorial binding of TFs to enhancers, dynamics of TF binding following stimulation, or the downstream effects on gene expression. Here, we address these questions in two types of myeloid antigen presenting cells (APCs), macrophages and dendritic cells (DCs), before and after stimulation with lipopolysaccharide (LPS), a potent stimulator of the innate immune response. RESULTS We classified enhancers according to the combination of TFs binding them. There were significant correlations between the sets of TFs bound to enhancers prior to stimulation and expression changes of nearby genes after stimulation. Importantly, a set of enhancers pre-bound by PU.1, C/EBPβ, ATF3, IRF4, and JunB was strongly associated with induced genes and binding by stimulus-activated regulators. Our classification suggests that transient loss of ATF3 binding to a subset of these enhancers is important for regulation of early-induced genes. Changes in TF-enhancer binding after stimulation were correlated with binding by additional activated TFs and with the presence of proximally located enhancers. CONCLUSIONS The results presented in this study reveal the complexity and dynamics of TF- enhancer binding before and after stimulation in myeloid APCs.
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Affiliation(s)
- Alexis Vandenbon
- Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
- Immuno-Genomics Research Unit, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
| | - Shunsuke Teraguchi
- Quantitative Immunology Research Unit, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
| | - Osamu Takeuchi
- Laboratory of Infection and Prevention, Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan
| | - Daron M Standley
- Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
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217
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Rabani M, Raychowdhury R, Jovanovic M, Rooney M, Stumpo DJ, Pauli A, Hacohen N, Schier AF, Blackshear PJ, Friedman N, Amit I, Regev A. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell 2014; 159:1698-710. [PMID: 25497548 DOI: 10.1016/j.cell.2014.11.015] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 09/09/2014] [Accepted: 10/22/2014] [Indexed: 10/24/2022]
Abstract
Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing sites; and transcription, processing, and degradation rates of each transcript at a splice junction resolution during the LPS response of mouse dendritic cells. Four key regulatory strategies, dominated by RNA transcription changes, generate most temporal gene expression patterns. Noncanonical strategies that also employ dynamic posttranscriptional regulation control only a minority of genes, but provide unique signal processing features. We validate Tristetraprolin (TTP) as a major regulator of RNA degradation in one noncanonical strategy. Applying DRiLL to the regulation of noncoding RNAs and to zebrafish embryogenesis demonstrates its broad utility. Our study provides a new quantitative approach to discover transcriptional and posttranscriptional events that control dynamic changes in transcript levels using RNA sequencing data.
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Affiliation(s)
- Michal Rabani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | | | - Marko Jovanovic
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Rooney
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard/MIT Division of Health Sciences and Technology, Cambridge, MA 02141, USA
| | - Deborah J Stumpo
- The Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Andrea Pauli
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nir Hacohen
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander F Schier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Perry J Blackshear
- The Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA; Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Nir Friedman
- School of Computer Science and Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
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218
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Gosselin D, Link VM, Romanoski CE, Fonseca GJ, Eichenfield DZ, Spann NJ, Stender JD, Chun HB, Garner H, Geissmann F, Glass CK. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell 2014; 159:1327-40. [PMID: 25480297 PMCID: PMC4364385 DOI: 10.1016/j.cell.2014.11.023] [Citation(s) in RCA: 936] [Impact Index Per Article: 93.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 11/16/2014] [Accepted: 11/17/2014] [Indexed: 12/20/2022]
Abstract
Macrophages reside in essentially all tissues of the body and play key roles in innate and adaptive immune responses. Distinct populations of tissue macrophages also acquire context-specific functions that are important for normal tissue homeostasis. To investigate mechanisms responsible for tissue-specific functions, we analyzed the transcriptomes and enhancer landscapes of brain microglia and resident macrophages of the peritoneal cavity. In addition, we exploited natural genetic variation as a genome-wide "mutagenesis" strategy to identify DNA recognition motifs for transcription factors that promote common or subset-specific binding of the macrophage lineage-determining factor PU.1. We find that distinct tissue environments drive divergent programs of gene expression by differentially activating a common enhancer repertoire and by inducing the expression of divergent secondary transcription factors that collaborate with PU.1 to establish tissue-specific enhancers. These findings provide insights into molecular mechanisms by which tissue environment influences macrophage phenotypes that are likely to be broadly applicable to other cell types.
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Affiliation(s)
- David Gosselin
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA; Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 82152, Germany
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Gregory J Fonseca
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Dawn Z Eichenfield
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Joshua D Stender
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Hyun B Chun
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Hannah Garner
- Centre for Molecular and Cellular Biology of Inflammation, King's College London, London SE1 1UL, UK; Peter Gorer Department of Immunobiology, King's College London, London SE1 1UL, UK
| | - Frederic Geissmann
- Centre for Molecular and Cellular Biology of Inflammation, King's College London, London SE1 1UL, UK; Peter Gorer Department of Immunobiology, King's College London, London SE1 1UL, UK
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA; Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
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219
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Fontana MF, Baccarella A, Pancholi N, Pufall MA, Herbert DR, Kim CC. JUNB is a key transcriptional modulator of macrophage activation. THE JOURNAL OF IMMUNOLOGY 2014; 194:177-86. [PMID: 25472994 DOI: 10.4049/jimmunol.1401595] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Activated macrophages are crucial for restriction of microbial infection but may also promote inflammatory pathology in a wide range of both infectious and sterile conditions. The pathways that regulate macrophage activation are therefore of great interest. Recent studies in silico have putatively identified key transcription factors that may control macrophage activation, but experimental validation is lacking. In this study, we generated a macrophage regulatory network from publicly available microarray data, employing steps to enrich for physiologically relevant interactions. Our analysis predicted a novel relationship between the AP-1 family transcription factor Junb and the gene Il1b, encoding the pyrogen IL-1β, which macrophages express upon activation by inflammatory stimuli. Previously, Junb has been characterized primarily as a negative regulator of the cell cycle, whereas AP-1 activity in myeloid inflammatory responses has largely been attributed to c-Jun. We confirmed experimentally that Junb is required for full expression of Il1b, and of additional genes involved in classical inflammation, in macrophages treated with LPS and other immunostimulatory molecules. Furthermore, Junb modulates expression of canonical markers of alternative activation in macrophages treated with IL-4. Our results demonstrate that JUNB is a significant modulator of both classical and alternative macrophage activation. Further, this finding provides experimental validation for our network modeling approach, which will facilitate the future use of gene expression data from open databases to reveal novel, physiologically relevant regulatory relationships.
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Affiliation(s)
- Mary F Fontana
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143; and
| | - Alyssa Baccarella
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143; and
| | - Nidhi Pancholi
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143; and
| | - Miles A Pufall
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - De'Broski R Herbert
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143; and
| | - Charles C Kim
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143; and
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220
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Krebs W, Schmidt SV, Goren A, De Nardo D, Labzin L, Bovier A, Ulas T, Theis H, Kraut M, Latz E, Beyer M, Schultze JL. Optimization of transcription factor binding map accuracy utilizing knockout-mouse models. Nucleic Acids Res 2014; 42:13051-60. [PMID: 25378309 PMCID: PMC4245947 DOI: 10.1093/nar/gku1078] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 09/26/2014] [Accepted: 10/16/2014] [Indexed: 12/20/2022] Open
Abstract
Genome-wide assessment of protein-DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify 'hyper ChIPable regions' as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses, particularly when developing ChIP-assays with novel antibody reagents.
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Affiliation(s)
- Wolfgang Krebs
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Susanne V Schmidt
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Alon Goren
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dominic De Nardo
- Institute of Innate Immunity, University Hospitals, University of Bonn, 53127 Bonn, Germany
| | - Larisa Labzin
- Institute of Innate Immunity, University Hospitals, University of Bonn, 53127 Bonn, Germany
| | - Anton Bovier
- Institute for Applied Mathematics, University of Bonn, 53115 Bonn, Germany
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Heidi Theis
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Michael Kraut
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University Hospitals, University of Bonn, 53127 Bonn, Germany Division of Infectious Diseases and Immunology, UMass Medical School, Worcester, MA 01605, USA German Center of Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
| | - Marc Beyer
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
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221
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Bornstein C, Winter D, Barnett-Itzhaki Z, David E, Kadri S, Garber M, Amit I. A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States. Mol Cell 2014; 56:749-62. [PMID: 25453760 DOI: 10.1016/j.molcel.2014.10.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/13/2014] [Accepted: 10/14/2014] [Indexed: 01/11/2023]
Abstract
During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into alternative cell fates are not fully understood. Here, we identify cell-fate-determining transcription factors (TFs) governing dendritic cell (DC) development by annotating the enhancer landscapes of the DC lineage. Combining these analyses with detailed overexpression, knockdown, and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, a pulse of TF expression can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes.
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Affiliation(s)
| | - Deborah Winter
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | | | - Eyal David
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Sabah Kadri
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology and Program in Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ido Amit
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
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222
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Abstract
Systems-level analysis of biological processes strives to comprehensively and quantitatively evaluate the interactions between the relevant molecular components over time, thereby enabling development of models that can be employed to ultimately predict behavior. Rapid development in measurement technologies (omics), when combined with the accessible nature of the cellular constituents themselves, is allowing the field of innate immunity to take significant strides toward this lofty goal. In this review, we survey exciting results derived from systems biology analyses of the immune system, ranging from gene regulatory networks to influenza pathogenesis and systems vaccinology.
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223
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Stockinger B, Di Meglio P, Gialitakis M, Duarte JH. The aryl hydrocarbon receptor: multitasking in the immune system. Annu Rev Immunol 2014; 32:403-32. [PMID: 24655296 DOI: 10.1146/annurev-immunol-032713-120245] [Citation(s) in RCA: 640] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The aryl hydrocarbon receptor (AhR), for many years almost exclusively studied by the pharmacology/toxicology field for its role in mediating the toxicity of xenobiotics such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), has more recently attracted the attention of immunologists. The evolutionary conservation of this transcription factor and its widespread expression in the immune system point to important physiological functions that are slowly being unraveled. In particular, the emphasis is now shifting from the role of AhR in the xenobiotic pathway toward its mode of action in response to physiological ligands. In this article, we review the current understanding of the molecular interactions and functions of AhR in the immune system in steady state and in the presence of infection and inflammation, with a focus on barrier organs such as the skin, the gut, and the lung.
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Affiliation(s)
- Brigitta Stockinger
- Division of Molecular Immunology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom; , , ,
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224
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Cohen M, Matcovitch O, David E, Barnett-Itzhaki Z, Keren-Shaul H, Blecher-Gonen R, Jaitin DA, Sica A, Amit I, Schwartz M. Chronic exposure to TGFβ1 regulates myeloid cell inflammatory response in an IRF7-dependent manner. EMBO J 2014; 33:2906-21. [PMID: 25385836 DOI: 10.15252/embj.201489293] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tissue microenvironment influences the function of resident and infiltrating myeloid-derived cells. In the central nervous system (CNS), resident microglia and freshly recruited infiltrating monocyte-derived macrophages (mo-MΦ) display distinct activities under pathological conditions, yet little is known about the microenvironment-derived molecular mechanism that regulates these differences. Here, we demonstrate that long exposure to transforming growth factor-β1 (TGFβ1) impaired the ability of myeloid cells to acquire a resolving anti-inflammatory phenotype. Using genome-wide expression analysis and chromatin immunoprecipitation followed by next-generation sequencing, we show that the capacity to undergo pro- to anti-inflammatory (M1-to-M2) phenotype switch is controlled by the transcription factor interferon regulatory factor 7 (IRF7) that is down-regulated by the TGFβ1 pathway. RNAi-mediated perturbation of Irf7 inhibited the M1-to-M2 switch, while IFNβ1 (an IRF7 pathway activator) restored it. In vivo induction of Irf7 expression in microglia, following spinal cord injury, reduced their pro-inflammatory activity. These results highlight the key role of tissue-specific environmental factors in determining the fate of resident myeloid-derived cells under both physiological and pathological conditions.
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Affiliation(s)
- Merav Cohen
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Orit Matcovitch
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Antonio Sica
- Humanitas Clinical and Research Center, Rozzano Milan, Italy DiSCAFF, University of Piemonte Orientale A. Avogadro, Novara, Italy
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Schwartz
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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225
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Genome-wide identification of hypoxia-inducible factor-1 and -2 binding sites in hypoxic human macrophages alternatively activated by IL-10. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:10-22. [PMID: 25450522 DOI: 10.1016/j.bbagrm.2014.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 10/21/2014] [Accepted: 10/29/2014] [Indexed: 12/14/2022]
Abstract
Macrophages (MΦ) often accumulate in hypoxic areas, where they significantly influence disease progression. Anti-inflammatory cytokines, such as IL-10, generate alternatively activated macrophages that support tumor growth. To understand how alternative activation affects the transcriptional profile of hypoxic macrophages, we globally mapped binding sites of hypoxia-inducible factor (HIF)-1α and HIF-2α in primary human monocyte-derived macrophages prestimulated with IL-10. 713 HIF-1 and 795 HIF-2 binding sites were identified under hypoxia. Pretreatment with IL-10 altered the binding pattern, with 120 new HIF-1 and 188 new HIF-2 binding sites emerging. HIF-1 binding was most prominent in promoters, while HIF-2 binding was more abundant in enhancer regions. Comparison of ChIP-seq data obtained in other cells revealed a highly cell type specific binding of HIF. In MΦ HIF binding occurred preferentially in already active enhancers or promoters. To assess the roles of HIF on gene expression, primary human macrophages were treated with siRNA against HIF-1α or HIF-2α, followed by genome-wide gene expression analysis. Comparing mRNA expression to the HIF binding profile revealed a significant enrichment of hypoxia-inducible genes previously identified by ChIP-seq. Analysis of gene expression under hypoxia alone and hypoxia/IL-10 showed the enhanced induction of a set of genes including PLOD2 and SLC2A3, while another group including KDM3A and ADM remained unaffected or was reduced by IL-10. Taken together IL-10 influences the DNA binding pattern of HIF and the level of gene induction.
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226
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Kim S, Becker J, Bechheim M, Kaiser V, Noursadeghi M, Fricker N, Beier E, Klaschik S, Boor P, Hess T, Hofmann A, Holdenrieder S, Wendland JR, Fröhlich H, Hartmann G, Nöthen MM, Müller-Myhsok B, Pütz B, Hornung V, Schumacher J. Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes. Nat Commun 2014; 5:5236. [PMID: 25327457 DOI: 10.1038/ncomms6236] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 09/11/2014] [Indexed: 12/18/2022] Open
Abstract
Toll-like receptors (TLRs) play a key role in innate immunity. Apart from their function in host defense, dysregulation in TLR signalling can confer risk to autoimmune diseases, septic shock or cancer. Here we report genetic variants and transcripts that are active only during TLR signalling and contribute to interindividual differences in immune response. Comparing unstimulated versus TLR4-stimulated monocytes reveals 1,471 expression quantitative trait loci (eQTLs) that are unique to TLR4 stimulation. Among these we find functional SNPs for the expression of NEU4, CCL14, CBX3 and IRF5 on TLR4 activation. Furthermore, we show that SNPs conferring risk to primary biliary cirrhosis (PBC), inflammatory bowel disease (IBD) and celiac disease are immune response eQTLs for PDGFB and IL18R1. Thus, PDGFB and IL18R1 represent plausible candidates for studying the pathophysiology of these disorders in the context of TLR4 activation. In summary, this study presents novel insights into the genetic basis of the innate immune response and exemplifies the value of eQTL studies in the context of exogenous cell stimulation.
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Affiliation(s)
- Sarah Kim
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany [3] Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Jessica Becker
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Matthias Bechheim
- Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Vera Kaiser
- Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nadine Fricker
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Esther Beier
- Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Sven Klaschik
- Department for Anesthesiology and Intensive Care Medicine, University of Bonn, Bonn 53127, Germany
| | - Peter Boor
- Institute of Pathology and Department of Nephrology, University Clinic of RWTH Aachen, Aachen 52074, Germany
| | - Timo Hess
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Andrea Hofmann
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Stefan Holdenrieder
- Institute for Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn 53127, Germany
| | - Jens R Wendland
- Worldwide R&D, Pfizer Inc., Cambridge, Massachusetts 02139, USA
| | - Holger Fröhlich
- Bonn-Aachen International Center for IT (B-IT), University of Bonn, Bonn 53113, Germany
| | - Gunther Hartmann
- Institute for Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn 53127, Germany
| | - Markus M Nöthen
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Bertram Müller-Myhsok
- 1] Statistical Genetics, Max Planck Institute of Psychiatry, Munich 80804, Germany [2] Munich Cluster for Systems Neurology (SyNergy), Munich 80804, Germany [3] Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK
| | - Benno Pütz
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Veit Hornung
- Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Johannes Schumacher
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
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227
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Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 2014; 159:440-55. [PMID: 25263330 PMCID: PMC4265475 DOI: 10.1016/j.cell.2014.09.014] [Citation(s) in RCA: 1308] [Impact Index Per Article: 130.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/08/2014] [Accepted: 09/08/2014] [Indexed: 02/06/2023]
Abstract
CRISPR-Cas9 is a versatile genome editing technology for studying the functions of genetic elements. To broadly enable the application of Cas9 in vivo, we established a Cre-dependent Cas9 knockin mouse. We demonstrated in vivo as well as ex vivo genome editing using adeno-associated virus (AAV)-, lentivirus-, or particle-mediated delivery of guide RNA in neurons, immune cells, and endothelial cells. Using these mice, we simultaneously modeled the dynamics of KRAS, p53, and LKB1, the top three significantly mutated genes in lung adenocarcinoma. Delivery of a single AAV vector in the lung generated loss-of-function mutations in p53 and Lkb1, as well as homology-directed repair-mediated Kras(G12D) mutations, leading to macroscopic tumors of adenocarcinoma pathology. Together, these results suggest that Cas9 mice empower a wide range of biological and disease modeling applications.
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Affiliation(s)
- Randall J Platt
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sidi Chen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yang Zhou
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael J Yim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lukasz Swiech
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hannah R Kempton
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James E Dahlman
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Oren Parnas
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas M Eisenhaure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Marko Jovanovic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Siddharth Jhunjhunwala
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthias Heidenreich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Guoping Feng
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Phillip A Sharp
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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228
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Luyten A, Zang C, Liu XS, Shivdasani RA. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells. Genes Dev 2014; 28:1827-39. [PMID: 25128499 PMCID: PMC4197967 DOI: 10.1101/gad.240101.114] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Tissues may adopt diverse strategies to establish specific transcriptional programs in daughter lineages. In blood, it is unclear when chromatin becomes permissive for transcription of genes expressed in distinct lineages. Luyten et al. present genome-wide analyses on chromatin dynamics and transcription factor binding at successive stages in primary mouse blood cell differentiation. The results reveal surprising features of enhancer delineation in a self-renewing tissue, distinct from the strategy applied in self-renewing intestinal crypts. This study provides a useful foundation to consider classical observations on cellular reprogramming and lineage plasticity in hematopoiesis. Tissues may adopt diverse strategies to establish specific transcriptional programs in daughter lineages. In intestinal crypts, enhancers for genes expressed in both major cell types appear broadly permissive in stem and specified progenitor cells. In blood, another self-renewing tissue, it is unclear when chromatin becomes permissive for transcription of genes expressed in distinct terminal lineages. Using chromatin immunoprecipitation (ChIP) combined with deep sequencing (ChIP-seq) to profile activating histone marks, we studied enhancer dynamics in primary mouse blood stem, progenitor, and specified cells. Stem and multipotent progenitor cells show scant H3K4me2 marking at enhancers bound by specific transcription factors in their committed progeny. Rather, enhancers are modulated dynamically and serially, with substantial loss and gain of H3K4me2, at each cellular transition. Quantitative analysis of these dynamics accurately modeled hematopoiesis according to Waddington’s notion of epigenotypes. Delineation of enhancers in terminal blood lineages coincides with cell specification, and enhancers active in single lineages show well-positioned H3K4me2- and H3K27ac-marked nucleosomes and DNaseI hypersensitivity in other cell types, revealing limited lineage fidelity. These findings demonstrate that enhancer chronology in blood cells differs markedly from that in intestinal crypts. Chromatin dynamics in hematopoiesis provide a useful foundation to consider classical observations such as cellular reprogramming and multilineage locus priming.
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Affiliation(s)
- Annouck Luyten
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Chongzhi Zang
- Department of Biostatistics and Computational Biology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts 02215, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts 02215, USA;
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
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229
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Carpenter S, Fitzgerald KA. Transcription of inflammatory genes: long noncoding RNA and beyond. J Interferon Cytokine Res 2014; 35:79-88. [PMID: 25250698 DOI: 10.1089/jir.2014.0120] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The innate immune system must coordinate elaborate signaling pathways to turn on expression of hundreds of genes to provide protection against pathogens and resolve acute inflammation. Multiple genes within distinct functional categories are coordinately and temporally regulated by transcriptional on and off switches in response to distinct external stimuli. Three classes of transcription factors act together with transcriptional coregulators and chromatin-modifying complexes to control these programs. In addition, newer studies implicate long noncoding RNA (lncRNA) as additional regulators of these responses. LncRNAs promote, fine-tune, and restrain the inflammatory program. In this study, we provide an overview of gene regulation and the emerging importance of lncRNAs in the immune system.
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Affiliation(s)
- Susan Carpenter
- 1 Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
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230
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Smale ST, Natoli G. Transcriptional control of inflammatory responses. Cold Spring Harb Perspect Biol 2014; 6:a016261. [PMID: 25213094 DOI: 10.1101/cshperspect.a016261] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The inflammatory response requires the activation of a complex transcriptional program that is both cell-type- and stimulus-specific and involves the dynamic regulation of hundreds of genes. In the context of an inflamed tissue, extensive changes in gene expression occur in both parenchymal cells and infiltrating cells of the immune system. Recently, basic transcriptional mechanisms that control inflammation have been clarified at a genome scale, particularly in macrophages and conventional dendritic cells. The regulatory logic of distinct groups of inflammatory genes can be explained to some extent by identifiable sequence-encoded features of their chromatin organization, which impact on transcription factor (TF) accessibility and impose different requirements for gene activation. Moreover, it has become apparent that the interplay between TFs activated by inflammatory stimuli and master regulators exerts a crucial role in controlling cell-type-specific transcriptional outputs.
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Affiliation(s)
- Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), I-20139 Milan, Italy
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231
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Albergante L, Blow JJ, Newman TJ. Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks. eLife 2014; 3:e02863. [PMID: 25182846 PMCID: PMC4151086 DOI: 10.7554/elife.02863] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 08/08/2014] [Indexed: 01/30/2023] Open
Abstract
The gene regulatory network (GRN) is the central decision-making module of the cell. We have developed a theory called Buffered Qualitative Stability (BQS) based on the hypothesis that GRNs are organised so that they remain robust in the face of unpredictable environmental and evolutionary changes. BQS makes strong and diverse predictions about the network features that allow stable responses under arbitrary perturbations, including the random addition of new connections. We show that the GRNs of E. coli, M. tuberculosis, P. aeruginosa, yeast, mouse, and human all verify the predictions of BQS. BQS explains many of the small- and large-scale properties of GRNs, provides conditions for evolvable robustness, and highlights general features of transcriptional response. BQS is severely compromised in a human cancer cell line, suggesting that loss of BQS might underlie the phenotypic plasticity of cancer cells, and highlighting a possible sequence of GRN alterations concomitant with cancer initiation.
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Affiliation(s)
- Luca Albergante
- College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - J Julian Blow
- College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Timothy J Newman
- College of Life Sciences, University of Dundee, Dundee, United Kingdom School of Engineering, Physics and Mathematics, University of Dundee, Dundee, United Kingdom
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232
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Role and therapeutic value of dendritic cells in central nervous system autoimmunity. Cell Death Differ 2014; 22:215-24. [PMID: 25168240 DOI: 10.1038/cdd.2014.125] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 06/23/2014] [Indexed: 12/20/2022] Open
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells that control the generation of adaptive immunity. Consequently, DCs have a central role in the induction of protective immunity to pathogens and also in the pathogenic immune response responsible for the development and progression of autoimmune disorders. Thus the study of the molecular pathways that control DC development and function is likely to result in new strategies for the therapeutic manipulation of the immune response. In this review, we discuss the role and therapeutic value of DCs in autoimmune diseases, with a special focus on multiple sclerosis.
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233
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Saliba DG, Heger A, Eames HL, Oikonomopoulos S, Teixeira A, Blazek K, Androulidaki A, Wong D, Goh FG, Weiss M, Byrne A, Pasparakis M, Ragoussis J, Udalova IA. IRF5:RelA interaction targets inflammatory genes in macrophages. Cell Rep 2014; 8:1308-17. [PMID: 25159141 PMCID: PMC4471814 DOI: 10.1016/j.celrep.2014.07.034] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 01/10/2014] [Accepted: 07/22/2014] [Indexed: 12/23/2022] Open
Abstract
Interferon Regulatory Factor 5 (IRF5) plays a major role in setting up an inflammatory macrophage phenotype, but the molecular basis of its transcriptional activity is not fully understood. In this study, we conduct a comprehensive genome-wide analysis of IRF5 recruitment in macrophages stimulated with bacterial lipopolysaccharide and discover that IRF5 binds to regulatory elements of highly transcribed genes. Analysis of protein:DNA microarrays demonstrates that IRF5 recognizes the canonical IRF-binding (interferon-stimulated response element [ISRE]) motif in vitro. However, IRF5 binding in vivo appears to rely on its interactions with other proteins. IRF5 binds to a noncanonical composite PU.1:ISRE motif, and its recruitment is aided by RelA. Global gene expression analysis in macrophages deficient in IRF5 and RelA highlights the direct role of the RelA:IRF5 cistrome in regulation of a subset of key inflammatory genes. We map the RelA:IRF5 interaction domain and suggest that interfering with it would offer selective targeting of macrophage inflammatory activities. Genome-wide function of IRF5 in LPS-stimulated macrophages was analyzed IRF5 cistrome overlaps with RelA cistrome at multiple loci IRF5 targets regulatory elements of highly inducible inflammatory genes IRF5 recruitment to key inflammatory loci is assisted by RelA
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Affiliation(s)
- David G Saliba
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX37FY, UK
| | - Andreas Heger
- CGAT, MRC Functional Genomics Unit, University of Oxford, South Parks Road, Oxford OX13PT, UK
| | - Hayley L Eames
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX37FY, UK
| | - Spyros Oikonomopoulos
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Ana Teixeira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Katrina Blazek
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX37FY, UK
| | - Ariadne Androulidaki
- Institute for Genetics, University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne 50931, Germany
| | - Daniel Wong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Fui G Goh
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX37FY, UK
| | - Miriam Weiss
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX37FY, UK
| | - Adam Byrne
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX37FY, UK
| | - Manolis Pasparakis
- Institute for Genetics, University of Cologne, Joseph-Stelzmann-Strasse 26, Cologne 50931, Germany
| | - Jiannis Ragoussis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Irina A Udalova
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX37FY, UK.
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234
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Zhao B, Barrera LA, Ersing I, Willox B, Schmidt SCS, Greenfeld H, Zhou H, Mollo SB, Shi TT, Takasaki K, Jiang S, Cahir-McFarland E, Kellis M, Bulyk ML, Kieff E, Gewurz BE. The NF-κB genomic landscape in lymphoblastoid B cells. Cell Rep 2014; 8:1595-606. [PMID: 25159142 DOI: 10.1016/j.celrep.2014.07.037] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 06/09/2014] [Accepted: 07/21/2014] [Indexed: 01/17/2023] Open
Abstract
The nuclear factor κB (NF-κΒ) subunits RelA, RelB, cRel, p50, and p52 are each critical for B cell development and function. To systematically characterize their responses to canonical and noncanonical NF-κB pathway activity, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) analysis in lymphoblastoid B cell lines (LCLs). We found a complex NF-κB-binding landscape, which did not readily reflect the two NF-κB pathway paradigms. Instead, 10 subunit-binding patterns were observed at promoters and 11 at enhancers. Nearly one-third of NF-κB-binding sites lacked κB motifs and were instead enriched for alternative motifs. The oncogenic forkhead box protein FOXM1 co-occupied nearly half of NF-κB-binding sites and was identified in protein complexes with NF-κB on DNA. FOXM1 knockdown decreased NF-κB target gene expression and ultimately induced apoptosis, highlighting FOXM1 as a synthetic lethal target in B cell malignancy. These studies provide a resource for understanding mechanisms that underlie NF-κB nuclear activity and highlight opportunities for selective NF-κB blockade.
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Affiliation(s)
- Bo Zhao
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Luis A Barrera
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ina Ersing
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Bradford Willox
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stefanie C S Schmidt
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Greenfeld
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hufeng Zhou
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah B Mollo
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tommy T Shi
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kaoru Takasaki
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sizun Jiang
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen Cahir-McFarland
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Elliott Kieff
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin E Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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235
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Seguín-Estévez Q, Dunand-Sauthier I, Lemeille S, Iseli C, Ibberson M, Ioannidis V, Schmid CD, Rousseau P, Barras E, Geinoz A, Xenarios I, Acha-Orbea H, Reith W. Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing. Nucleic Acids Res 2014; 42:9641-55. [PMID: 25104025 PMCID: PMC4150779 DOI: 10.1093/nar/gku674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The activation, or maturation, of dendritic cells (DCs) is crucial for the initiation of adaptive T-cell mediated immune responses. Research on the molecular mechanisms implicated in DC maturation has focused primarily on inducible gene-expression events promoting the acquisition of new functions, such as cytokine production and enhanced T-cell-stimulatory capacity. In contrast, mechanisms that modulate DC function by inducing widespread gene-silencing remain poorly understood. Yet the termination of key functions is known to be critical for the function of activated DCs. Genome-wide analysis of activation-induced histone deacetylation, combined with genome-wide quantification of activation-induced silencing of nascent transcription, led us to identify a novel inducible transcriptional-repression pathway that makes major contributions to the DC-maturation process. This silencing response is a rapid primary event distinct from repression mechanisms known to operate at later stages of DC maturation. The repressed genes function in pivotal processes--including antigen-presentation, extracellular signal detection, intracellular signal transduction and lipid-mediator biosynthesis--underscoring the central contribution of the silencing mechanism to rapid reshaping of DC function. Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this lineage-specific transcription factor in marking genes poised for inducible repression.
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Affiliation(s)
- Queralt Seguín-Estévez
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Isabelle Dunand-Sauthier
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Sylvain Lemeille
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Christian Iseli
- Vital-IT, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Mark Ibberson
- Vital-IT, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | | | - Christoph D Schmid
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, CH-4051 Basel, Switzerland University of Basel, CH-4051 Basel, Switzerland
| | - Philippe Rousseau
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Antoine Geinoz
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Ioannis Xenarios
- Vital-IT, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Hans Acha-Orbea
- Department of Biochemistry, Faculty of Biology and Medicine, University of Lausanne, CH-1066 Epalinges, Switzerland
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
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236
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Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E, Keren-Shaul H, Mildner A, Winter D, Jung S, Friedman N, Amit I. Immunogenetics. Chromatin state dynamics during blood formation. Science 2014; 345:943-9. [PMID: 25103404 DOI: 10.1126/science.1256271] [Citation(s) in RCA: 565] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chromatin modifications are crucial for development, yet little is known about their dynamics during differentiation. Hematopoiesis provides a well-defined model to study chromatin state dynamics; however, technical limitations impede profiling of homogeneous differentiation intermediates. We developed a high-sensitivity indexing-first chromatin immunoprecipitation approach to profile the dynamics of four chromatin modifications across 16 stages of hematopoietic differentiation. We identify 48,415 enhancer regions and characterize their dynamics. We find that lineage commitment involves de novo establishment of 17,035 lineage-specific enhancers. These enhancer repertoire expansions foreshadow transcriptional programs in differentiated cells. Combining our enhancer catalog with gene expression profiles, we elucidate the transcription factor network controlling chromatin dynamics and lineage specification in hematopoiesis. Together, our results provide a comprehensive model of chromatin dynamics during development.
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Affiliation(s)
- David Lara-Astiaso
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Weiner
- Institute of Life Sciences, The Hebrew University, Jerusalem, Israel. School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
| | | | - Irina Zaretsky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Mildner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Friedman
- Institute of Life Sciences, The Hebrew University, Jerusalem, Israel. School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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237
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Wackerhage H, Del Re DP, Judson RN, Sudol M, Sadoshima J. The Hippo signal transduction network in skeletal and cardiac muscle. Sci Signal 2014; 7:re4. [PMID: 25097035 DOI: 10.1126/scisignal.2005096] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The discovery of the Hippo pathway can be traced back to two areas of research. Genetic screens in fruit flies led to the identification of the Hippo pathway kinases and scaffolding proteins that function together to suppress cell proliferation and tumor growth. Independent research, often in the context of muscle biology, described Tead (TEA domain) transcription factors, which bind CATTCC DNA motifs to regulate gene expression. These two research areas were joined by the finding that the Hippo pathway regulates the activity of Tead transcription factors mainly through phosphorylation of the transcriptional coactivators Yap and Taz, which bind to and activate Teads. Additionally, many other signal transduction proteins crosstalk to members of the Hippo pathway forming a Hippo signal transduction network. We discuss evidence that the Hippo signal transduction network plays important roles in myogenesis, regeneration, muscular dystrophy, and rhabdomyosarcoma in skeletal muscle, as well as in myogenesis, organ size control, and regeneration of the heart. Understanding the role of Hippo kinases in skeletal and heart muscle physiology could have important implications for translational research.
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Affiliation(s)
- Henning Wackerhage
- School of Medical Sciences, University of Aberdeen, Health Sciences Building, Foresterhill, AB25 2ZD Aberdeen, Scotland, UK.
| | - Dominic P Del Re
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers University, 185 South Orange Avenue, Newark, NJ 07103, USA
| | - Robert N Judson
- School of Medical Sciences, University of Aberdeen, Health Sciences Building, Foresterhill, AB25 2ZD Aberdeen, Scotland, UK. Biomedical Research Centre, University of British Columbia, 317-2194 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Marius Sudol
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, Singapore 117411, Republic of Singapore. Department of Medicine, Mount Sinai School of Medicine, One Gustave Levy Place, New York, NY 10029, USA
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers University, 185 South Orange Avenue, Newark, NJ 07103, USA
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238
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Raza S, Barnett MW, Barnett-Itzhaki Z, Amit I, Hume DA, Freeman TC. Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators. J Leukoc Biol 2014; 96:167-83. [PMID: 24721704 PMCID: PMC4378362 DOI: 10.1189/jlb.6hi0313-169r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 01/17/2014] [Accepted: 02/23/2014] [Indexed: 01/09/2023] Open
Abstract
Macrophages respond to the TLR4 agonist LPS with a sequential transcriptional cascade controlled by a complex regulatory network of signaling pathways and transcription factors. At least two distinct pathways are currently known to be engaged by TLR4 and are distinguished by their dependence on the adaptor molecule MyD88. We have used gene expression microarrays to define the effects of each of three variables--LPS dose, LPS versus IFN-β and -γ, and genetic background--on the transcriptional response of mouse BMDMs. Analysis of correlation networks generated from the data has identified subnetworks or modules within the macrophage transcriptional network that are activated selectively by these variables. We have identified mouse strain-specific signatures, including a module enriched for SLE susceptibility candidates. In the modules of genes unique to different treatments, we found a module of genes induced by type-I IFN but not by LPS treatment, suggesting another layer of complexity in the LPS-TLR4 signaling feedback control. We also observe that the activation of the complement system, in common with the known activation of MHC class 2 genes, is reliant on IFN-γ signaling. Taken together, these data further highlight the exquisite nature of the regulatory systems that control macrophage activation, their likely relevance to disease resistance/susceptibility, and the appropriate response of these cells to proinflammatory stimuli.
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Affiliation(s)
- Sobia Raza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Scotland, United Kingdom; and
| | - Mark W Barnett
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Scotland, United Kingdom; and
| | | | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Scotland, United Kingdom; and
| | - Tom C Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Scotland, United Kingdom; and
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239
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When genetics meets epigenetics: deciphering the mechanisms controlling inter-individual variation in immune responses to infection. Curr Opin Immunol 2014; 29:119-26. [PMID: 24981784 DOI: 10.1016/j.coi.2014.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/31/2014] [Accepted: 06/04/2014] [Indexed: 11/23/2022]
Abstract
The response of host immune cells to microbial stimuli is dependent on robust and coordinated gene expression programs involving the transcription of thousands of genes. The dysregulation of such regulatory programs is likely to significantly contribute to the marked differences in susceptibility to infectious diseases observed among individuals and between human populations. Although the specific factors leading to a dysfunctional immune response to infection remain largely unknown, we are increasingly appreciating the importance of genetic variants in altering the expression levels of immune-related genes, possibly via epigenetic changes. This review describes how recent technological advances have profoundly contributed to our current understanding of the genetic architecture and the epigenetic rules controlling immune responses to infectious agents and how genetic and epigenetic data can be combined to unravel the mechanisms associated with host variation in transcriptional responses to infection.
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240
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Chauvistré H, Küstermann C, Rehage N, Klisch T, Mitzka S, Felker P, Rose-John S, Zenke M, Seré KM. Dendritic cell development requires histone deacetylase activity. Eur J Immunol 2014; 44:2478-88. [PMID: 24810486 PMCID: PMC4209797 DOI: 10.1002/eji.201344150] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 04/08/2014] [Accepted: 04/30/2014] [Indexed: 01/24/2023]
Abstract
DCs develop from multipotent progenitors (MPPs), which commit into DC-restricted common dendritic cell progenitors (CDPs). CDPs further differentiate into classical DCs (cDCs) and plasmacytoid DCs (pDCs). Here, we studied the impact of histone acetylation on DC development in C57BL/6 mice by interfering with histone acetylation and deacetylation, employing histone deacetylase (HDAC) inhibitors. We observed that commitment of MPPs into CDPs was attenuated by HDAC inhibition and that pDC development was specifically blocked. Gene expression profiling revealed that HDAC inhibition prevents establishment of a DC-specific gene expression repertoire. Importantly, protein levels of the core DC transcription factor PU.1 were reduced in HDAC inhibitor-treated cells and consequently PU.1 recruitment at PU.1 target genes Fms-like tyrosine kinase 3 (Flt3), interferon regulatory factor 8 (IRF8), and PU.1 itself was impaired. Thus, our results demonstrate that attenuation of PU.1 expression by HDAC inhibition causes reduced expression of key DC regulators, which results in attenuation of DC development. We propose that chromatin modifiers, such as HDACs, are required for establishing a DC gene network, where Flt3/STAT3 signaling drives PU.1 and IRF8 expression and DC development. Taken together, our study identifies HDACs as critical regulators of DC lineage commitment and development.
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Affiliation(s)
- Heike Chauvistré
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Medical School, Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
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241
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Gasper WC, Marinov GK, Pauli-Behn F, Scott MT, Newberry K, DeSalvo G, Ou S, Myers RM, Vielmetter J, Wold BJ. Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: identifying ChIP-quality p300 monoclonal antibodies. Sci Rep 2014; 4:5152. [PMID: 24919486 PMCID: PMC4053718 DOI: 10.1038/srep05152] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/13/2014] [Indexed: 01/11/2023] Open
Abstract
Chromatin immunoprecipitation coupled with DNA sequencing (ChIP-seq) is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It identifies sites of transcription factor, cofactor and RNA polymerase occupancy, as well as the distribution of histone marks. Consortia such as the ENCyclopedia Of DNA Elements (ENCODE) have produced large datasets using manual protocols. However, future measurements of hundreds of additional factors in many cell types and physiological states call for higher throughput and consistency afforded by automation. Such automation advances, when provided by multiuser facilities, could also improve the quality and efficiency of individual small-scale projects. The immunoprecipitation process has become rate-limiting, and is a source of substantial variability when performed manually. Here we report a fully automated robotic ChIP (R-ChIP) pipeline that allows up to 96 reactions. A second bottleneck is the dearth of renewable ChIP-validated immune reagents, which do not yet exist for most mammalian transcription factors. We used R-ChIP to screen new mouse monoclonal antibodies raised against p300, a histone acetylase, well-known as a marker of active enhancers, for which ChIP-competent monoclonal reagents have been lacking. We identified, validated for ChIP-seq, and made publicly available a monoclonal reagent called ENCITp300-1.
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Affiliation(s)
- William C Gasper
- 1] Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA [2]
| | - Georgi K Marinov
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Max T Scott
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Gilberto DeSalvo
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Susan Ou
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jost Vielmetter
- 1] Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA [2]
| | - Barbara J Wold
- 1] Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA [2]
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242
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Semiconductor-based DNA sequencing of histone modification states. Nat Commun 2014; 4:2672. [PMID: 24157732 PMCID: PMC3917140 DOI: 10.1038/ncomms3672] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 09/26/2013] [Indexed: 12/14/2022] Open
Abstract
The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing and targeted re-sequencing. Here we demonstrate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP-seq on the Ion Torrent platform. We leverage this method for epigenetic profiling of tumour tissues.
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243
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Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 2014; 510:363-9. [PMID: 24919153 PMCID: PMC4193940 DOI: 10.1038/nature13437] [Citation(s) in RCA: 683] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 05/02/2014] [Indexed: 12/23/2022]
Abstract
High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript's level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a 'core' module of antiviral genes is expressed very early by a few 'precocious' cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced 'peaked' inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses.
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Affiliation(s)
- Alex K Shalek
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA [3] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [4]
| | - Rahul Satija
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2]
| | - Joe Shuga
- 1] Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA [2]
| | - John J Trombetta
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Dave Gennert
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Diana Lu
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Peilin Chen
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Rona S Gertner
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Jellert T Gaublomme
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Nir Yosef
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Schraga Schwartz
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Brian Fowler
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Suzanne Weaver
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Jing Wang
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Xiaohui Wang
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Ruihua Ding
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Raktima Raychowdhury
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Nir Friedman
- School of Computer Science and Engineering, Hebrew University, 91904 Jerusalem, Israel
| | - Nir Hacohen
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Center for Immunology and Inflammatory Diseases & Department of Medicine, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Hongkun Park
- 1] Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA [2] Department of Physics, Harvard University, 17 Oxford Street, Cambridge, Massachusetts 02138, USA [3] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Andrew P May
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, California 94080, USA
| | - Aviv Regev
- 1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA
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244
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Calero-Nieto FJ, Ng FS, Wilson NK, Hannah R, Moignard V, Leal-Cervantes AI, Jimenez-Madrid I, Diamanti E, Wernisch L, Göttgens B. Key regulators control distinct transcriptional programmes in blood progenitor and mast cells. EMBO J 2014; 33:1212-26. [PMID: 24760698 PMCID: PMC4168288 DOI: 10.1002/embj.201386825] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 02/27/2014] [Accepted: 03/20/2014] [Indexed: 12/21/2022] Open
Abstract
Despite major advances in the generation of genome-wide binding maps, the mechanisms by which transcription factors (TFs) regulate cell type identity have remained largely obscure. Through comparative analysis of 10 key haematopoietic TFs in both mast cells and blood progenitors, we demonstrate that the largely cell type-specific binding profiles are not opportunistic, but instead contribute to cell type-specific transcriptional control, because (i) mathematical modelling of differential binding of shared TFs can explain differential gene expression, (ii) consensus binding sites are important for cell type-specific binding and (iii) knock-down of blood stem cell regulators in mast cells reveals mast cell-specific genes as direct targets. Finally, we show that the known mast cell regulators Mitf and c-fos likely contribute to the global reorganisation of TF binding profiles. Taken together therefore, our study elucidates how key regulatory TFs contribute to transcriptional programmes in several distinct mammalian cell types.
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Affiliation(s)
- Fernando J Calero-Nieto
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Felicia S Ng
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Rebecca Hannah
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Victoria Moignard
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Ana I Leal-Cervantes
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Isabel Jimenez-Madrid
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Lorenz Wernisch
- MRC Biostatistics Unit, Institute of Public Health, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
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245
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Paul F, Amit I. Plasticity in the transcriptional and epigenetic circuits regulating dendritic cell lineage specification and function. Curr Opin Immunol 2014; 30:1-8. [PMID: 24820527 DOI: 10.1016/j.coi.2014.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/09/2014] [Indexed: 12/23/2022]
Abstract
Dendritic cells (DC) are critical and functionally versatile innate immune sentinels. Here, we coarsely partition the adult DC lineage into three developmental subtypes and argue that pioneer transcription factors and chromatin remodeling are responsible for specification and plasticity between the DC subsets. Subsequently, intricate signaling-dependent transcription factor networks generate different functional states in response to pathogen stimuli within a specified DC subtype. To expand our understanding of lineage heterogeneity and functional activation states, we discuss the use of single cell genomics approaches in the context of a newly emerging systems immunology era, complementing the dichotomous definition of immune cells based solely on their surface marker expression. Rapid developments in single cell genomics are beginning to provide us with robust tools to potentially revise the working models of DC specification and the common hematopoietic tree.
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Affiliation(s)
- Franziska Paul
- 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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246
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Afek A, Lukatsky DB. Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites. Biophys J 2014; 105:1653-60. [PMID: 24094406 DOI: 10.1016/j.bpj.2013.08.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Revised: 08/04/2013] [Accepted: 08/26/2013] [Indexed: 01/01/2023] Open
Abstract
Recent experiments provide an unprecedented view of protein-DNA binding in yeast and human genomes at single-nucleotide resolution. These measurements, performed over large cell populations, show quite generally that sequence-specific transcription regulators with well-defined protein-DNA consensus motifs bind only a fraction among all consensus motifs present in the genome. Alternatively, proteins in vivo often bind DNA regions lacking known consensus sequences. The rules determining whether a consensus motif is functional remain incompletely understood. Here we predict that genomic background surrounding specific protein-DNA binding motifs statistically modulates the binding of sequence-specific transcription regulators to these motifs. In particular, we show that nonconsensus protein-DNA binding in yeast is statistically enhanced, on average, around functional Reb1 motifs that are bound as compared to nonfunctional Reb1 motifs that are unbound. The landscape of nonconsensus protein-DNA binding around functional CTCF motifs in human demonstrates a more complex behavior. In particular, human genomic regions characterized by the highest CTCF occupancy, show statistically reduced level of nonconsensus protein-DNA binding. Our findings suggest that nonconsensus protein-DNA binding is fine-tuned around functional binding sites using a variety of design strategies.
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Affiliation(s)
- Ariel Afek
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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247
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Rothenberg EV. The chromatin landscape and transcription factors in T cell programming. Trends Immunol 2014; 35:195-204. [PMID: 24703587 PMCID: PMC4039984 DOI: 10.1016/j.it.2014.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/02/2014] [Accepted: 03/03/2014] [Indexed: 12/24/2022]
Abstract
T cell development from multipotent progenitors to specialized effector subsets of mature T cells is guided by the iterative action of transcription factors. At each stage, transcription factors interact not only with an existing landscape of histone modifications and nucleosome packing, but also with other bound factors, while they modify the landscape for later-arriving factors in ways that fundamentally affect the control of gene expression. This review covers insights from genome-wide analyses of transcription factor binding and resulting chromatin conformation changes that reveal roles of cytokine signaling in effector T cell programming, the ways in which one factor can completely transform the impacts of previously bound factors, and the ways in which the baseline chromatin landscape is established during early T cell lineage commitment.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125 USA.
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248
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Gjidoda A, Tagore M, McAndrew MJ, Woods A, Floer M. Nucleosomes are stably evicted from enhancers but not promoters upon induction of certain pro-inflammatory genes in mouse macrophages. PLoS One 2014; 9:e93971. [PMID: 24705533 PMCID: PMC3976374 DOI: 10.1371/journal.pone.0093971] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/12/2014] [Indexed: 11/18/2022] Open
Abstract
Chromatin is thought to act as a barrier for binding of cis-regulatory transcription factors (TFs) to their sites on DNA and recruitment of the transcriptional machinery. Here we have analyzed changes in nucleosome occupancy at the enhancers as well as at the promoters of three pro-inflammatory genes when they are induced by bacterial lipopolysaccharides (LPS) in primary mouse macrophages. We find that nucleosomes are removed from the distal enhancers of IL12B and IL1A, as well as from the distal and proximal enhancers of IFNB1, and that clearance of enhancers correlates with binding of various cis-regulatory TFs. We further show that for IFNB1 the degree of nucleosome removal correlates well with the level of induction of the gene under different conditions. Surprisingly, we find that nucleosome occupancy at the promoters of IL12B and IL1A does not change significantly when the genes are induced, and that a considerably fraction of the cells is occupied by nucleosomes at any given time. We hypothesize that competing nucleosomes at the promoters of IL12B and IL1A may play a role in limiting the size of transcriptional bursts in individual cells, which may be important for controlling cytokine production in a population of immune cells.
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Affiliation(s)
- Alison Gjidoda
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Mohita Tagore
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Michael J. McAndrew
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Alexander Woods
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Monique Floer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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249
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Villar D, Flicek P, Odom DT. Evolution of transcription factor binding in metazoans - mechanisms and functional implications. Nat Rev Genet 2014; 15:221-33. [PMID: 24590227 PMCID: PMC4175440 DOI: 10.1038/nrg3481] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Differences in transcription factor binding can contribute to organismal evolution by altering downstream gene expression programmes. Genome-wide studies in Drosophila melanogaster and mammals have revealed common quantitative and combinatorial properties of in vivo DNA binding, as well as marked differences in the rate and mechanisms of evolution of transcription factor binding in metazoans. Here, we review the recently discovered rapid 're-wiring' of in vivo transcription factor binding between related metazoan species and summarize general principles underlying the observed patterns of evolution. We then consider what might explain the differences in genome evolution between metazoan phyla and outline the conceptual and technological challenges facing this research field.
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Affiliation(s)
- Diego Villar
- University of Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB1 01SD, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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250
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Feuerborn A, Mathow D, Srivastava PK, Gretz N, Gröne HJ. Basonuclin-1 modulates epithelial plasticity and TGF-β1-induced loss of epithelial cell integrity. Oncogene 2014; 34:1185-95. [PMID: 24662832 DOI: 10.1038/onc.2014.54] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/03/2014] [Accepted: 01/06/2014] [Indexed: 02/06/2023]
Abstract
Transforming growth factor-β1 (TGF-β1) is a multifunctional cytokine and critically involved in the progression of a variety of cancers. TGF-β1 signaling can impair tumor development by its anti-proliferative and pro-apoptotic features. In contrast, it may actively promote tumor progression and cancer cell dissemination by inducing a gradual switch from epithelial towards mesenchymal-like cell features (EMT-like), including decreased intercellular adhesion. Here, we show that expression of the transcription factor Basonuclin-1 (Bnc1) modulates TGF-β1-induced epithelial dedifferentiation of mammary epithelial cells. RNAi-mediated repression of Bnc1 resulted in enhanced intercellular adhesion and strongly impaired TGF-β1-dependent sheet disintegration and cell scattering. In contrast, forced expression of Bnc1 modifies plasma membrane/cytoskeletal dynamics and seemingly interferes with the initiation of sustainable cell-cell contacts. Follow-up analyses revealed that Bnc1 affects the expression of numerous TGF-β1-responsive genes including distinct EMT-related transcription factors, some of which modulate the expression of Bnc1 themselves. These results suggest that Bnc1 is part of a transcription factor network related to epithelial plasticity with reciprocal feedback-loop connections on which Smad-factors integrate TGF-β1 signaling. Our study demonstrates that Bnc1 regulates epithelial plasticity of mammary epithelial cells and influences outcome of TGF-β1 signaling.
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Affiliation(s)
- A Feuerborn
- Department of Cellular and Molecular Pathology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - D Mathow
- Department of Cellular and Molecular Pathology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - P K Srivastava
- Physiological Genomics and Medicine, MRC Clinical Sciences, Imperial College, London, UK
| | - N Gretz
- Department of Medical Research, Faculty of Medicine, Medical Research Centre (ZMF), University of Heidelberg, Mannheim, Germany
| | - H-J Gröne
- Department of Cellular and Molecular Pathology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
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