51
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Blais A. Myogenesis in the Genomics Era. J Mol Biol 2015; 427:2023-38. [DOI: 10.1016/j.jmb.2015.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 01/06/2023]
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52
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Handley A, Schauer T, Ladurner A, Margulies C. Designing Cell-Type-Specific Genome-wide Experiments. Mol Cell 2015; 58:621-31. [DOI: 10.1016/j.molcel.2015.04.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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53
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Cell death in development: Signaling pathways and core mechanisms. Semin Cell Dev Biol 2015; 39:12-9. [PMID: 25668151 DOI: 10.1016/j.semcdb.2015.02.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 01/22/2015] [Accepted: 02/02/2015] [Indexed: 11/20/2022]
Abstract
Programmed cell death eliminates unneeded and dangerous cells in a timely and effective manner during development. In this review, we examine the role cell death plays during development in worms, flies and mammals. We discuss signaling pathways that regulate developmental cell death, and describe how they communicate with the core cell death pathways. In most organisms, the majority of developmental cell death is seen in the nervous system. Therefore we focus on what is known about the regulation of developmental cell death in this tissue. Understanding how the cell death is regulated during development may provide insight into how this process can be manipulated in the treatment of disease.
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54
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Steiner FA, Henikoff S. Cell type-specific affinity purification of nuclei for chromatin profiling in whole animals. Methods Mol Biol 2015; 1228:3-14. [PMID: 25311117 DOI: 10.1007/978-1-4939-1680-1_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Analyzing cell differentiation during development in a complex organism requires the analysis of expression and chromatin profiles in individual cell types. Our laboratory has developed a simple and generally applicable strategy to purify specific cell types from whole organisms for simultaneous analysis of chromatin and expression. The method, termed INTACT for Isolation of Nuclei TAgged in specific Cell Types, depends on the expression of an affinity-tagged nuclear envelope protein in the cell type of interest. These nuclei can be affinity-purified from the total pool of nuclei and used as a source for RNA and chromatin. The method serves as a simple and scalable alternative to FACS sorting or laser capture microscopy to circumvent the need for expensive equipment and specialized skills. This chapter provides detailed protocols for the cell-type specific purification of nuclei from Caenorhabditis elegans.
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Affiliation(s)
- Florian A Steiner
- Basic Sciences Division, Howard Hughes Medical Institute, Seattle, WA, USA,
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55
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Shin J, Ming GL, Song H. Decoding neural transcriptomes and epigenomes via high-throughput sequencing. Nat Neurosci 2014; 17:1463-75. [PMID: 25349913 DOI: 10.1038/nn.3814] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/14/2014] [Indexed: 02/07/2023]
Abstract
The mammalian brain is an evolutionary marvel in which engraving and re-engraving of cellular states enable complex information processing and lifelong maintenance. Understanding the mechanisms by which neurons alter and maintain their molecular signatures during information processing is a fundamental goal of neuroscience. Next-generation sequencing (NGS) technology is rapidly transforming the ability to probe the molecular basis of neuronal function. NGS can define not only the complete molecular signatures of cells by transcriptome analyses but also the cascade of events that induce or maintain such signatures by epigenetic analyses. Here we offer some general and practical information to demystify NGS technology and highlight its potential to the neuroscience field. We start with discussion of the complexity of the nervous system, then introduce various applications of NGS with practical considerations and describe basic principles underlying various NGS technologies. Finally, we discuss emerging NGS-related technologies for the neuroscience field.
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Affiliation(s)
- Jaehoon Shin
- 1] Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [2] Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Guo-li Ming
- 1] Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [2] Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [3] Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [4] The Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hongjun Song
- 1] Graduate Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [2] Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [3] Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [4] The Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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56
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Gilsbach R, Preissl S, Grüning BA, Schnick T, Burger L, Benes V, Würch A, Bönisch U, Günther S, Backofen R, Fleischmann BK, Schübeler D, Hein L. Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease. Nat Commun 2014; 5:5288. [PMID: 25335909 PMCID: PMC4220495 DOI: 10.1038/ncomms6288] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 09/17/2014] [Indexed: 01/20/2023] Open
Abstract
The heart is a highly specialized organ with essential function for the organism throughout life. The significance of DNA methylation in shaping the phenotype of the heart remains only partially known. Here we generate and analyse DNA methylomes from highly purified cardiomyocytes of neonatal, adult healthy and adult failing hearts. We identify large genomic regions that are differentially methylated during cardiomyocyte development and maturation. Demethylation of cardiomyocyte gene bodies correlates strongly with increased gene expression. Silencing of demethylated genes is characterized by the polycomb mark H3K27me3 or by DNA methylation. De novo methylation by DNA methyltransferases 3A/B causes repression of fetal cardiac genes, including essential components of the cardiac sarcomere. Failing cardiomyocytes partially resemble neonatal methylation patterns. This study establishes DNA methylation as a highly dynamic process during postnatal growth of cardiomyocytes and their adaptation to pathological stress in a process tightly linked to gene regulation and activity. DNA methylation is essential for proper gene expression, development and genome stability. Here the authors present whole-genome DNA methylation analyses of purified mouse cardiomyocytes from newborn, adult and failing hearts and find highly dynamic patterns between the three phenotypes of cardiomyocytes.
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Affiliation(s)
- Ralf Gilsbach
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Sebastian Preissl
- 1] Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany [2] Hermann Staudinger Graduate School, University of Freiburg, Albertstrasse 21, 79104 Freiburg, Germany
| | - Björn A Grüning
- 1] Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany [2] Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, University of Freiburg, Hermann-Herder-Strasse 9, 79104 Freiburg, Germany
| | - Tilman Schnick
- 1] Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany [2] University Heart Center Freiburg/Bad Krozingen, Department of Congenital Heart Defects and Paediatric Cardiology, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - Lukas Burger
- 1] Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland [2] Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Vladimir Benes
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Andreas Würch
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Ulrike Bönisch
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Stefan Günther
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, University of Freiburg, Hermann-Herder-Strasse 9, 79104 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Bernd K Fleischmann
- Institute of Physiology I, Life and Brain Center, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Dirk Schübeler
- 1] Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland [2] University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Lutz Hein
- 1] Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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57
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Bheda P, Schneider R. Epigenetics reloaded: the single-cell revolution. Trends Cell Biol 2014; 24:712-23. [PMID: 25283892 DOI: 10.1016/j.tcb.2014.08.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 01/15/2023]
Abstract
Mechanistically, how epigenetic states are inherited through cellular divisions remains an important open question in the chromatin field and beyond. Defining the heritability of epigenetic states and the underlying chromatin-based mechanisms within a population of cells is complicated due to cell heterogeneity combined with varying levels of stability of these states; thus, efforts must be focused toward single-cell analyses. The approaches presented here constitute the forefront of epigenetics research at the single-cell level using classic and innovative methods to dissect epigenetics mechanisms from the limited material available in a single cell. This review further outlines exciting future avenues of research to address the significance of epigenetic heterogeneity and the contributions of microfluidics technologies to single-cell isolation and analysis.
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Affiliation(s)
- Poonam Bheda
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104/Inserm U964/Université de Strasbourg, 67400 Illkirch, France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104/Inserm U964/Université de Strasbourg, 67400 Illkirch, France.
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58
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Otsuki L, Cheetham SW, Brand AH. Freedom of expression: cell-type-specific gene profiling. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2014; 3:429-43. [PMID: 25174322 DOI: 10.1002/wdev.149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/10/2014] [Indexed: 12/17/2022]
Abstract
Cell fate and behavior are results of differential gene regulation, making techniques to profile gene expression in specific cell types highly desirable. Many methods now enable investigation at the DNA, RNA and protein level. This review introduces the most recent and popular techniques, and discusses key issues influencing the choice between these such as ease, cost and applicability of information gained. Interdisciplinary collaborations will no doubt contribute further advances, including not just in single cell type but single-cell expression profiling.
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Affiliation(s)
- Leo Otsuki
- The Gurdon Institute and Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, UK
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59
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Enhancer loops appear stable during development and are associated with paused polymerase. Nature 2014; 512:96-100. [PMID: 25043061 DOI: 10.1038/nature13417] [Citation(s) in RCA: 364] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/29/2014] [Indexed: 12/11/2022]
Abstract
Developmental enhancers initiate transcription and are fundamental to our understanding of developmental networks, evolution and disease. Despite their importance, the properties governing enhancer-promoter interactions and their dynamics during embryogenesis remain unclear. At the β-globin locus, enhancer-promoter interactions appear dynamic and cell-type specific, whereas at the HoxD locus they are stable and ubiquitous, being present in tissues where the target genes are not expressed. The extent to which preformed enhancer-promoter conformations exist at other, more typical, loci and how transcription is eventually triggered is unclear. Here we generated a high-resolution map of enhancer three-dimensional contacts during Drosophila embryogenesis, covering two developmental stages and tissue contexts, at unprecedented resolution. Although local regulatory interactions are common, long-range interactions are highly prevalent within the compact Drosophila genome. Each enhancer contacts multiple enhancers, and promoters with similar expression, suggesting a role in their co-regulation. Notably, most interactions appear unchanged between tissue context and across development, arising before gene activation, and are frequently associated with paused RNA polymerase. Our results indicate that the general topology governing enhancer contacts is conserved from flies to humans and suggest that transcription initiates from preformed enhancer-promoter loops through release of paused polymerase.
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60
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Wamstad JA, Wang X, Demuren OO, Boyer LA. Distal enhancers: new insights into heart development and disease. Trends Cell Biol 2014; 24:294-302. [DOI: 10.1016/j.tcb.2013.10.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 10/27/2013] [Accepted: 10/30/2013] [Indexed: 01/01/2023]
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61
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Abstract
Recent data support the view that epigenetic processes play a role in memory consolidation and help to transmit acquired memories even across generations in a Lamarckian manner. Drugs that target the epigenetic machinery were found to enhance memory function in rodents and ameliorate disease phenotypes in models for brain diseases such as Alzheimer's disease, Chorea Huntington, Depression or Schizophrenia. In this review, I will give an overview on the current knowledge of epigenetic processes in memory function and brain disease with a focus on Morbus Alzheimer as the most common neurodegenerative disease. I will address the question whether an epigenetic therapy could indeed be a suitable therapeutic avenue to treat brain diseases and discuss the necessary steps that should help to take neuroepigenetic research to the next level.
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Affiliation(s)
- Andre Fischer
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
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62
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Amin NM, Greco TM, Kuchenbrod LM, Rigney MM, Chung MI, Wallingford JB, Cristea IM, Conlon FL. Proteomic profiling of cardiac tissue by isolation of nuclei tagged in specific cell types (INTACT). Development 2014; 141:962-73. [PMID: 24496632 DOI: 10.1242/dev.098327] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The proper dissection of the molecular mechanisms governing the specification and differentiation of specific cell types requires isolation of pure cell populations from heterogeneous tissues and whole organisms. Here, we describe a method for purification of nuclei from defined cell or tissue types in vertebrate embryos using INTACT (isolation of nuclei tagged in specific cell types). This method, previously developed in plants, flies and worms, utilizes in vivo tagging of the nuclear envelope with biotin and the subsequent affinity purification of the labeled nuclei. In this study we successfully purified nuclei of cardiac and skeletal muscle from Xenopus using this strategy. We went on to demonstrate the utility of this approach by coupling the INTACT approach with liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic methodologies to profile proteins expressed in the nuclei of developing hearts. From these studies we have identified the Xenopus orthologs of 12 human proteins encoded by genes, which when mutated in human lead to congenital heart disease. Thus, by combining these technologies we are able to identify tissue-specific proteins that are expressed and required for normal vertebrate organ development.
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Affiliation(s)
- Nirav M Amin
- University of North Carolina McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA
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63
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Marion-Poll L, Montalban E, Munier A, Hervé D, Girault JA. Fluorescence-activated sorting of fixed nuclei: a general method for studying nuclei from specific cell populations that preserves post-translational modifications. Eur J Neurosci 2014; 39:1234-44. [DOI: 10.1111/ejn.12506] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/02/2014] [Accepted: 01/08/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Lucile Marion-Poll
- Inserm UMR-S 839; Paris France
- Université Pierre & Marie Curie; Sorbonne Universités; Paris France
- Institut du Fer à Moulin; Paris France
| | - Enrica Montalban
- Inserm UMR-S 839; Paris France
- Université Pierre & Marie Curie; Sorbonne Universités; Paris France
- Institut du Fer à Moulin; Paris France
| | - Annie Munier
- Université Pierre & Marie Curie; Sorbonne Universités; Paris France
- Cell Imaging and Flow Cytometry Facility; IFR83; Paris France
| | - Denis Hervé
- Inserm UMR-S 839; Paris France
- Université Pierre & Marie Curie; Sorbonne Universités; Paris France
- Institut du Fer à Moulin; Paris France
| | - Jean-Antoine Girault
- Inserm UMR-S 839; Paris France
- Université Pierre & Marie Curie; Sorbonne Universités; Paris France
- Institut du Fer à Moulin; Paris France
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64
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Ma J, Weake VM. Affinity-based isolation of tagged nuclei from Drosophila tissues for gene expression analysis. J Vis Exp 2014. [PMID: 24686501 DOI: 10.3791/51418] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Drosophila melanogaster embryonic and larval tissues often contain a highly heterogeneous mixture of cell types, which can complicate the analysis of gene expression in these tissues. Thus, to analyze cell-specific gene expression profiles from Drosophila tissues, it may be necessary to isolate specific cell types with high purity and at sufficient yields for downstream applications such as transcriptional profiling and chromatin immunoprecipitation. However, the irregular cellular morphology in tissues such as the central nervous system, coupled with the rare population of specific cell types in these tissues, can pose challenges for traditional methods of cell isolation such as laser microdissection and fluorescence-activated cell sorting (FACS). Here, an alternative approach to characterizing cell-specific gene expression profiles using affinity-based isolation of tagged nuclei, rather than whole cells, is described. Nuclei in the specific cell type of interest are genetically labeled with a nuclear envelope-localized EGFP tag using the Gal4/UAS binary expression system. These EGFP-tagged nuclei can be isolated using antibodies against GFP that are coupled to magnetic beads. The approach described in this protocol enables consistent isolation of nuclei from specific cell types in the Drosophila larval central nervous system at high purity and at sufficient levels for expression analysis, even when these cell types comprise less than 2% of the total cell population in the tissue. This approach can be used to isolate nuclei from a wide variety of Drosophila embryonic and larval cell types using specific Gal4 drivers, and may be useful for isolating nuclei from cell types that are not suitable for FACS or laser microdissection.
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Affiliation(s)
- Jingqun Ma
- Department of Biochemistry, Purdue University
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65
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Fischer A. Targeting histone-modifications in Alzheimer's disease. What is the evidence that this is a promising therapeutic avenue? Neuropharmacology 2014; 80:95-102. [PMID: 24486385 DOI: 10.1016/j.neuropharm.2014.01.038] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 01/06/2023]
Abstract
Alzheimer' s disease (AD) is the most common form of dementia causing an increasing emotional and economical burden to our societies. Although much progress has been made regarding the molecular mechanisms that underlie AD pathogenesis effective therapies are not available yet. The emerging field of neuroepigenetics has provided evidence that de-regulation of epigenetic processes play a role in AD. In this article we will critically review the primary research data that led to the hypothesis that targeting histone-modifying enzymes could be used to treat AD pathogenesis and address the question if the field is ready to translate such findings into clinical application.
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Affiliation(s)
- Andre Fischer
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Grisebachstr. 5, 37077 Göttingen, Germany; Research Group for Epigenetic Mechansims of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Grisebachstr. 5, 37077 Göttingen, Germany.
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66
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Polychronidou M, Lohmann I. Hox transcriptomics in Drosophila embryos. Methods Mol Biol 2014; 1196:197-208. [PMID: 25151165 DOI: 10.1007/978-1-4939-1242-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Hox proteins are evolutionarily conserved homeodomain containing transcription factors that specify segment identities along the anteroposterior axis of almost all bilaterian animals. They exert their morphogenetic role by transcriptionally regulating a large battery of downstream target genes. Therefore the dissection of transcriptional networks regulated by Hox proteins is an essential step towards a mechanistic understanding of how these transcription factors coordinate multiple developmental and morphogenetic processes. High-throughput techniques allowing whole-transcriptome mRNA expression profiling are powerful tools for the genome-wide identification of Hox downstream target genes in a variety of experimental settings. Here, we describe how to quantitatively identify Hox downstream genes in Drosophila embryos by performing a Hox transcriptome analysis using microarrays.
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Affiliation(s)
- Maria Polychronidou
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
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67
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Abstract
Chromatin immunoprecipitation (ChIP) is a technique that reveals in vivo location of a protein bound to DNA. ChIP coupled with DNA microarrays (ChIP-chip) or next-generation sequencing (ChIP-seq) allows for identification of binding sites of transcription factors on a global scale. Here we describe a protocol for ChIP to identify binding of the Ultrabithorax (Ubx) Hox transcription factors from imaginal discs of Drosophila larvae. The protocol can be extended to other model organisms and transcription factors.
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Affiliation(s)
- Pavan Agrawal
- Janelia Farm Research Campus, HHMI, Ashburn, VA, 20147, USA,
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68
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Southall TD, Gold KS, Egger B, Davidson CM, Caygill EE, Marshall OJ, Brand AH. Cell-type-specific profiling of gene expression and chromatin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells. Dev Cell 2013; 26:101-12. [PMID: 23792147 PMCID: PMC3714590 DOI: 10.1016/j.devcel.2013.05.020] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/20/2013] [Accepted: 05/24/2013] [Indexed: 12/20/2022]
Abstract
Cell-type-specific transcriptional profiling often requires the isolation of specific cell types from complex tissues. We have developed “TaDa,” a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation, or affinity purification. The method is simple, sensitive, highly reproducible, and transferable to any model system. We show that TaDa can be used to identify transcribed genes in a cell-type-specific manner with considerable temporal precision, enabling the identification of differential gene expression between neuroblasts and the neuroepithelial cells from which they derive. We profile the genome-wide binding of RNA polymerase II in these adjacent, clonally related stem cells within intact Drosophila brains. Our data reveal expression of specific metabolic genes in neuroepithelial cells, but not in neuroblasts, and highlight gene regulatory networks that may pattern neural stem cell fates. TaDa is a method for cell-type-specific profiling of chromatin binding proteins TaDa does not require cell sorting, fixation, or affinity purification This is a highly sensitive and robust technique for transcriptional profiling We report differential RNA Pol II binding in clonally related stem cells
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Affiliation(s)
- Tony D Southall
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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69
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Differential effects of cocaine on histone posttranslational modifications in identified populations of striatal neurons. Proc Natl Acad Sci U S A 2013; 110:9511-6. [PMID: 23690581 DOI: 10.1073/pnas.1307116110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Drugs of abuse, such as cocaine, induce changes in gene expression and epigenetic marks including alterations in histone posttranslational modifications in striatal neurons. These changes are thought to participate in physiological memory mechanisms and to be critical for long-term behavioral alterations. However, the striatum is composed of multiple cell types, including two distinct populations of medium-sized spiny neurons, and little is known concerning the cell-type specificity of epigenetic modifications. To address this question we used bacterial artificial chromosome transgenic mice, which express EGFP fused to the N-terminus of the large subunit ribosomal protein L10a driven by the D1 or D2 dopamine receptor (D1R, D2R) promoter, respectively. Fluorescence in nucleoli was used to sort nuclei from D1R- or D2R-expressing neurons and to quantify by flow cytometry the cocaine-induced changes in histone acetylation and methylation specifically in these two types of nuclei. The two populations of medium-sized spiny neurons displayed different patterns of histone modifications 15 min or 24 h after a single injection of cocaine or 24 h after seven daily injections. In particular, acetylation of histone 3 on Lys 14 and of histone 4 on Lys 5 and 12, and methylation of histone 3 on Lys 9 exhibited distinct and persistent changes in the two cell types. Our data provide insights into the differential epigenetic responses to cocaine in D1R- and D2R-positive neurons and their potential regulation, which may participate in the persistent effects of cocaine in these neurons. The method described should have general utility for studying nuclear modifications in different types of neuronal or nonneuronal cell types.
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70
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Bogdanović O, Fernández-Miñán A, Tena JJ, de la Calle-Mustienes E, Gómez-Skarmeta JL. The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos. Methods 2013; 62:207-15. [PMID: 23624103 DOI: 10.1016/j.ymeth.2013.04.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 04/05/2013] [Accepted: 04/15/2013] [Indexed: 01/08/2023] Open
Abstract
Genome-wide profiling of DNA methylation and histone modifications answered many questions as to how the genes are regulated on a global scale and what their epigenetic makeup is. Yet, little is known about the function of these marks during early vertebrate embryogenesis. Here we provide detailed protocols for ChIP-seq and MethylCap-seq procedures applied to zebrafish (Danio rerio) embryonic material at four developmental stages. As a proof of principle, we have profiled on a global scale a number of post-translational histone modifications including H3K4me1, H3K4me3 and H3K27ac. We demonstrate that these marks are dynamic during early development and that such developmental transitions can be detected by ChIP-seq. In addition, we applied MethylCap-seq to show that developmentally-regulated DNA methylation remodeling can be detected by such a procedure. Our MethylCap-seq data concur with previous DNA methylation studies of early zebrafish development rendering this method highly suitable for the global assessment of DNA methylation in early vertebrate embryos.
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Affiliation(s)
- Ozren Bogdanović
- Centro Andaluz de Biología del Desarrollo-CABD, CSIC-UPO-JA, 41013 Sevilla, Spain
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71
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High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc 2013; 8:539-54. [PMID: 23429716 DOI: 10.1038/nprot.2013.023] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Dynamic protein binding to DNA elements regulates genome function and cell fate. Although methods for mapping in vivo protein-DNA interactions are becoming crucial for every aspect of genomic research, they are laborious and costly, thereby limiting progress. Here we present a protocol for mapping in vivo protein-DNA interactions using a high-throughput chromatin immunoprecipitation (HT-ChIP) approach. By using paramagnetic beads, we streamline the entire ChIP and indexed library construction process: sample transfer and loss is minimized and the need for manually labor-intensive procedures such as washes, gel extraction and DNA precipitation is eliminated. All of this allows for fully automated, cost effective and highly sensitive 96-well ChIP sequencing (ChIP-seq). Sample preparation takes 3 d from cultured cells to pooled libraries. Compared with previous methods, HT-ChIP is more suitable for large-scale in vivo studies, specifically those measuring the dynamics of a large number of different chromatin modifications/transcription factors or multiple perturbations.
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