101
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Placek K, Schultze JL, Aschenbrenner AC. Epigenetic reprogramming of immune cells in injury, repair, and resolution. J Clin Invest 2019; 129:2994-3005. [PMID: 31329166 DOI: 10.1172/jci124619] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Immune cells are pivotal in the reaction to injury, whereupon, under ideal conditions, repair and resolution phases restore homeostasis following initial acute inflammation. Immune cell activation and reprogramming require transcriptional changes that can only be initiated if epigenetic alterations occur. Recently, accelerated deciphering of epigenetic mechanisms has extended knowledge of epigenetic regulation, including long-distance chromatin remodeling, DNA methylation, posttranslational histone modifications, and involvement of small and long noncoding RNAs. Epigenetic changes have been linked to aspects of immune cell development, activation, and differentiation. Furthermore, genome-wide epigenetic landscapes have been established for some immune cells, including tissue-resident macrophages, and blood-derived cells including T cells. The epigenetic mechanisms underlying developmental steps from hematopoietic stem cells to fully differentiated immune cells led to development of epigenetic technologies and insights into general rules of epigenetic regulation. Compared with more advanced research areas, epigenetic reprogramming of immune cells in injury remains in its infancy. While the early epigenetic mechanisms supporting activation of the immune response to injury have been studied, less is known about resolution and repair phases and cell type-specific changes. We review prominent recent findings concerning injury-mediated epigenetic reprogramming, particularly in stroke and myocardial infarction. Lastly, we illustrate how single-cell technologies will be crucial to understanding epigenetic reprogramming in the complex sequential processes following injury.
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Affiliation(s)
- Katarzyna Placek
- Immunology and Metabolism, LIMES Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany.,Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
| | - Anna C Aschenbrenner
- Genomics and Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany
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102
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Wang Y, Wang A, Liu Z, Thurman AL, Powers LS, Zou M, Zhao Y, Hefel A, Li Y, Zabner J, Au KF. Single-molecule long-read sequencing reveals the chromatin basis of gene expression. Genome Res 2019; 29:1329-1342. [PMID: 31201211 PMCID: PMC6673713 DOI: 10.1101/gr.251116.119] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/10/2019] [Indexed: 11/25/2022]
Abstract
Genome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remain poorly studied at the single-cell level. Here, we present a new experimental approach, methyltransferase treatment followed by single-molecule long-read sequencing (MeSMLR-seq), for long-range mapping of nucleosomes and chromatin accessibility at single DNA molecules and thus achieve comprehensive-coverage characterization of the corresponding heterogeneity. MeSMLR-seq offers direct measurements of both nucleosome-occupied and nucleosome-evicted regions on a single DNA molecule, which is challenging for many existing methods. We applied MeSMLR-seq to haploid yeast, where single DNA molecules represent single cells, and thus we could investigate the combinatorics of many (up to 356) nucleosomes at long range in single cells. We illustrated the differential organization principles of nucleosomes surrounding the transcription start site for silent and actively transcribed genes, at the single-cell level and in the long-range scale. The heterogeneous patterns of chromatin status spanning multiple genes were phased. Together with single-cell RNA-seq data, we quantitatively revealed how chromatin accessibility correlated with gene transcription positively in a highly heterogeneous scenario. Moreover, we quantified the openness of promoters and investigated the coupled chromatin changes of adjacent genes at single DNA molecules during transcription reprogramming. In addition, we revealed the coupled changes of chromatin accessibility for two neighboring glucose transporter genes in response to changes in glucose concentration.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Anqi Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Zujun Liu
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew L Thurman
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Linda S Powers
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Meng Zou
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Adam Hefel
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Yunyi Li
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Joseph Zabner
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA.,Department of Biostatistics, University of Iowa, Iowa City, Iowa 52242, USA
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103
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NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule. Sci Rep 2019; 9:8140. [PMID: 31148571 PMCID: PMC6544651 DOI: 10.1038/s41598-019-44597-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/20/2019] [Indexed: 11/15/2022] Open
Abstract
Recent technical advances highlight that to understand mammalian development and human disease we need to consider transcriptional and epigenetic cell-to-cell differences within cell populations. This is particularly important in key areas of biomedicine like stem cell differentiation and intratumor heterogeneity. The recently developed nucleosome occupancy and methylome (NOMe) assay facilitates the simultaneous study of DNA methylation and nucleosome positioning on the same DNA strand. NOMe-treated DNA can be sequenced by sanger (NOMe-PCR) or high throughput approaches (NOMe-seq). NOMe-PCR provides information for a single locus at the single molecule while NOMe-seq delivers genome-wide data that is usually interrogated to obtain population-averaged measures. Here, we have developed a bioinformatic tool that allow us to easily obtain locus-specific information at the single molecule using genome-wide NOMe-seq datasets obtained from bulk populations. We have used NOMePlot to study mouse embryonic stem cells and found that polycomb-repressed bivalent gene promoters coexist in two different epigenetic states, as defined by the nucleosome binding pattern detected around their transcriptional start site.
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104
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Nucleosome positioning and spacing: from genome-wide maps to single arrays. Essays Biochem 2019; 63:5-14. [PMID: 31015380 DOI: 10.1042/ebc20180058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 01/07/2023]
Abstract
The positioning of nucleosomes relative to DNA and their neighboring nucleosomes represents a fundamental layer of chromatin organization. Changes in nucleosome positioning and spacing affect the accessibility of DNA to regulatory factors and the formation of higher order chromatin structures. Sequencing of mononucleosomal fragments allowed mapping nucleosome positions on a genome-wide level in many organisms. This revealed that successions of evenly spaced and well-positioned nucleosomes-so called phased nucleosome arrays-occur at the 5' end of many active genes and in the vicinity of transcription factor and other protein binding sites. Phased arrays arise from the interplay of barrier elements on the DNA, which position adjacent nucleosomes, and the nucleosome spacing activity of ATP-dependent chromatin remodelers. A shortcoming of classic mononucleosomal mapping experiments is that they only reveal nucleosome spacing and array regularity at select sites in the genome with well-positioned nucleosomes. However, new technological approaches elucidate nucleosome array structure throughout the genome and with single-cell resolution. In the future, it will be interesting to see whether changes in nucleosome array regularity and spacing contribute to the formation of higher order chromatin structures and the spatial organization of the genome in vivo.
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105
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Chromatin fiber structural motifs as regulatory hubs of genome function? Essays Biochem 2019; 63:123-132. [PMID: 30967476 PMCID: PMC6484786 DOI: 10.1042/ebc20180065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 02/07/2023]
Abstract
Nucleosomes cover eukaryotic genomes like beads on a string and play a central role in regulating genome function. Isolated strings of nucleosomes have the potential to compact and form higher order chromatin structures, such as the well-characterized 30-nm fiber. However, despite tremendous advances in observing chromatin fibers in situ it has not been possible to confirm that regularly ordered fibers represent a prevalent structural level in the folding of chromosomes. Instead, it appears that folding at a larger scale than the nucleosome involves a variety of random structures with fractal characteristics. Nevertheless, recent progress provides evidence for the existence of structural motifs in chromatin fibers, potentially localized to strategic sites in the genome. Here we review the current understanding of chromatin fiber folding and the emerging roles that oligonucleosomal motifs play in the regulation of genome function.
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106
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Kurup JT, Campeanu IJ, Kidder BL. Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing. Epigenetics Chromatin 2019; 12:20. [PMID: 30940185 PMCID: PMC6444878 DOI: 10.1186/s13072-019-0266-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Positioning of nucleosomes along DNA is an integral regulator of chromatin accessibility and gene expression in diverse cell types. However, the precise nature of how histone demethylases including the histone 3 lysine 4 (H3K4) demethylase, KDM5B, impacts nucleosome positioning around transcriptional start sites (TSS) of active genes is poorly understood. RESULTS Here, we report that KDM5B is a critical regulator of nucleosome positioning in embryonic stem (ES) cells. Micrococcal nuclease sequencing (MNase-Seq) revealed increased enrichment of nucleosomes around TSS regions and DNase I hypersensitive sites in KDM5B-depleted ES cells. Moreover, depletion of KDM5B resulted in a widespread redistribution and disorganization of nucleosomes in a sequence-dependent manner. Dysregulated nucleosome phasing was also evident in KDM5B-depleted ES cells, including asynchronous nucleosome spacing surrounding TSS regions, where nucleosome variance was positively correlated with the degree of asynchronous phasing. The redistribution of nucleosomes around TSS regions in KDM5B-depleted ES cells is correlated with dysregulated gene expression, and altered H3K4me3 and RNA polymerase II occupancy. In addition, we found that DNA shape features varied significantly at regions with shifted nucleosomes. CONCLUSION Altogether, our data support a role for KDM5B in regulating nucleosome positioning in ES cells.
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Affiliation(s)
- Jiji T. Kurup
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
| | - Ion J. Campeanu
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
| | - Benjamin L. Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI USA
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107
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Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. Nat Methods 2019; 16:323-325. [PMID: 30923384 DOI: 10.1038/s41592-019-0361-7] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/20/2019] [Indexed: 12/17/2022]
Abstract
Our method for analyzing histone modifications, scChIC-seq (single-cell chromatin immunocleavage sequencing), involves targeting of the micrococcal nuclease (MNase) to a histone mark of choice by tethering to a specific antibody. Cleaved target sites are then selectively PCR amplified. We show that scChIC-seq reliably detects H3K4me3 and H3K27me3 target sites in single human white blood cells. The resulting data are used for clustering of blood cell types.
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108
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Chen X, Miragaia RJ, Natarajan KN, Teichmann SA. A rapid and robust method for single cell chromatin accessibility profiling. Nat Commun 2018; 9:5345. [PMID: 30559361 PMCID: PMC6297232 DOI: 10.1038/s41467-018-07771-0] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/13/2018] [Indexed: 11/30/2022] Open
Abstract
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) is widely used to identify regulatory regions throughout the genome. However, very few studies have been performed at the single cell level (scATAC-seq) due to technical challenges. Here we developed a simple and robust plate-based scATAC-seq method, combining upfront bulk Tn5 tagging with single-nuclei sorting. We demonstrate that our method works robustly across various systems, including fresh and cryopreserved cells from primary tissues. By profiling over 3000 splenocytes, we identify distinct immune cell types and reveal cell type-specific regulatory regions and related transcription factors.
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Affiliation(s)
- Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ricardo J Miragaia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- MedImmune, Sir Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Kedar Nath Natarajan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Functional Biology and Metabolism Unit, Biochemistry and Molecular Biology, SDU, 5230, Odense, Denmark
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge, CB3 0HE, UK.
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109
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From Cellular Diversity to the Roots of Variability. Cell 2018; 175:1169-1171. [PMID: 30445033 DOI: 10.1016/j.cell.2018.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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110
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Clyde D. Spotlight on nucleosomes. Nat Rev Genet 2018; 19:738-739. [PMID: 30367164 DOI: 10.1038/s41576-018-0070-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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