1
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Fu Z, Jiang S, Sun Y, Zheng S, Zong L, Li P. Cut&tag: a powerful epigenetic tool for chromatin profiling. Epigenetics 2024; 19:2293411. [PMID: 38105608 PMCID: PMC10730171 DOI: 10.1080/15592294.2023.2293411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. Chromatin immunoprecipitation is the most popular and powerful approach for mapping chromatin, and other enzyme-tethering techniques have recently become available for living cells. Among these, Cleavage Under Targets and Tagmentation (CUT&Tag) is a relatively novel chromatin profiling method that has rapidly gained popularity in the field of epigenetics since 2019. It has also been widely adapted to map chromatin modifications and TFs in different species, illustrating the association of these chromatin epitopes with various physiological and pathological processes. Scalable single-cell CUT&Tag can be combined with distinct platforms to distinguish cellular identity, epigenetic features and even spatial chromatin profiling. In addition, CUT&Tag has been developed as a strategy for joint profiling of the epigenome, transcriptome or proteome on the same sample. In this review, we will mainly consolidate the applications of CUT&Tag and its derivatives on different platforms, give a detailed explanation of the pros and cons of this technique as well as the potential development trends and applications in the future.
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Affiliation(s)
- Zhijun Fu
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Sanjie Jiang
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Yiwen Sun
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Shanqiao Zheng
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Liang Zong
- BGI Tech Solutions Co, Ltd. BGI-Wuhan, Wuhan, China
| | - Peipei Li
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
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2
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Daly AE, Schiffman A, Hoffmann A, Smale ST. Examining NF-κB genomic interactions by ChIP-seq and CUT&Tag. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.11.607521. [PMID: 39185161 PMCID: PMC11343132 DOI: 10.1101/2024.08.11.607521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
An understanding of the mechanisms and logic by which transcription factors coordinate gene regulation requires delineation of their genomic interactions at a genome-wide scale. Chromatin immunoprecipitation-sequencing (ChIP-seq) and more recent techniques, including CUT&Tag, typically reveal thousands of genomic interactions by transcription factors, but without insight into their functional roles. Due to cost and time considerations, optimization of ChIP experimental conditions is typically carried out only with representative interaction sites rather than through genome-wide analyses. Here, we describe insights gained from the titration of two chemical crosslinking reagents in genome-wide ChIP-seq experiments examining two members of the NF-κB family of transcription factors: RelA and c-Rel. We also describe a comparison of ChIP-seq and CUT&Tag. Our results highlight the large impact of ChIP-seq experimental conditions on the number of interactions detected, on the enrichment of consensus and non-consensus DNA motifs for the factor, and on the frequency with which the genomic interactions detected are located near potential target genes. We also found considerable consistency between ChIP-seq and CUT&Tag results, but with a substantial fraction of genomic interactions detected with only one of the two techniques. Together, the results demonstrate the dramatic impact of experimental conditions on the results obtained in a genome-wide analysis of transcription factor binding, highlighting the need for further scrutiny of the functional significance of these condition-dependent differences.
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Affiliation(s)
- Allison E. Daly
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Allison Schiffman
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095, USA
| | - Stephen T. Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
- Department of Medicine, University of California, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA
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3
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Pepin AS, Schneider R. Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins. EMBO Rep 2024; 25:3202-3220. [PMID: 39095610 PMCID: PMC11316037 DOI: 10.1038/s44319-024-00199-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/10/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024] Open
Abstract
In eukaryotes, DNA is packaged into chromatin with the help of highly conserved histone proteins. Together with DNA-binding proteins, posttranslational modifications (PTMs) on these histones play crucial roles in regulating genome function, cell fate determination, inheritance of acquired traits, cellular states, and diseases. While most studies have focused on individual DNA-binding proteins, chromatin proteins, or histone PTMs in bulk cell populations, such chromatin features co-occur and potentially act cooperatively to accomplish specific functions in a given cell. This review discusses state-of-the-art techniques for the simultaneous profiling of multiple chromatin features in low-input samples and single cells, focusing on histone PTMs, DNA-binding, and chromatin proteins. We cover the origins of the currently available toolkits, compare and contrast their characteristic features, and discuss challenges and perspectives for future applications. Studying the co-occurrence of histone PTMs, DNA-binding proteins, and chromatin proteins in single cells will be central for a better understanding of the biological relevance of combinatorial chromatin features, their impact on genomic output, and cellular heterogeneity.
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Affiliation(s)
- Anne-Sophie Pepin
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany.
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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4
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Fadri MTM, Lee JB, Keung AJ. Summary of ChIP-Seq Methods and Description of an Optimized ChIP-Seq Protocol. Methods Mol Biol 2024; 2842:419-447. [PMID: 39012609 DOI: 10.1007/978-1-0716-4051-7_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Chromatin immunoprecipitation (ChIP) is an invaluable method to characterize interactions between proteins and genomic DNA, such as the genomic localization of transcription factors and post-translational modification of histones. DNA and proteins are reversibly and covalently crosslinked using formaldehyde. Then the cells are lysed to release the chromatin. The chromatin is fragmented into smaller sizes either by micrococcal nuclease (MN) or sonication and then purified from other cellular components. The protein-DNA complexes are enriched by immunoprecipitation (IP) with antibodies that target the epitope of interest. The DNA is released from the proteins by heat and protease treatment, followed by degradation of contaminating RNAs with RNase. The resulting DNA is analyzed using various methods, including polymerase chain reaction (PCR), quantitative PCR (qPCR), or sequencing. This protocol outlines each of these steps for both yeast and human cells. This chapter includes a contextual discussion of the combination of ChIP with DNA analysis methods such as ChIP-on-Chip, ChIP-qPCR, and ChIP-Seq, recent updates on ChIP-Seq data analysis pipelines, complementary methods for identification of binding sites of DNA binding proteins, and additional protocol information about ChIP-qPCR and ChIP-Seq.
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Affiliation(s)
- Maria Theresa M Fadri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Jessica B Lee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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5
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Blanco E, Ballaré C, Di Croce L, Aranda S. Quantitative Comparison of Multiple Chromatin Immunoprecipitation-Sequencing (ChIP-seq) Experiments with spikChIP. Methods Mol Biol 2023; 2624:55-72. [PMID: 36723809 DOI: 10.1007/978-1-0716-2962-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The chromatin immunoprecipitation coupled with the next-generation sequencing (ChIP-seq) is a powerful technique that enables to characterize the genomic distribution of chromatin-associated proteins, histone posttranslational modifications, and histone variants. However, in the absence of a reference control for monitoring experimental and biological variations, the standard ChIP-seq scheme is unable to accurately assess changes in the abundance of chromatin targets across different experimental samples. To overcome this limitation, the combination of external spike-in material with the experimental chromatin is offered as an effective solution for quantitative comparison of ChIP-seq data across different conditions. Here, we detail (i) the experimental protocol for preparing quality control spike-in chromatin from Drosophila melanogaster cells and (ii) the computational protocol to compare ChIP-seq samples with spike-in based on the use of the spikChIP software.
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Affiliation(s)
- Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
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6
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Kahiapo JK, Monahan K. Chromatin Immunoprecipitation from Formaldehyde Cross-Linked Olfactory Sensory Neurons. Methods Mol Biol 2023; 2710:71-82. [PMID: 37688725 DOI: 10.1007/978-1-0716-3425-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2023]
Abstract
Chromatin immunoprecipitation (ChIP) allows a researcher to determine the genomic occupancy of nuclear proteins, providing insight into the roles of transcription factors, chromatin modifiers, histone modifications, and other factors bound to DNA. Protein-DNA interactions are first fixed in vivo by chemical cross-linking, and then a target protein is captured together with any associated DNA by an antibody mediated pull-down. The co-immunoprecipitated DNA can then be assayed by quantitative PCR or deep sequencing. Here, we demonstrate this technique using murine olfactory sensory neurons (OSNs) purified using fluorescence-activated cell sorting (FACS) and antibodies for the ubiquitous chromatin protein CTCF.
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Affiliation(s)
- Jerome K Kahiapo
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Kevin Monahan
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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7
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Yan Y, Huang T. The Interactome of Protein, DNA, and RNA. Methods Mol Biol 2023; 2695:89-110. [PMID: 37450113 DOI: 10.1007/978-1-0716-3346-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Proteins participate in many processes of the organism and are very important for maintaining the health of the organism. However, proteins cannot function independently in the body. They must interact with proteins, DNA, RNA, and other substances to perform biological functions and maintain the body's health. At present, there are many experimental methods and software tools that can detect and predict the interaction between proteins and other substances. There are also many databases that record the interaction between proteins and other substances. This article mainly describes protein-protein, protein-DNA, and protein-RNA interactions in detail by introducing some commonly used experimental methods, the software tools produced with the accumulation of experimental data and the rapid development of machine learning, and the related databases that record the relationship between proteins and some substances. By this review, we hope that through the analysis and summary of various aspects, it will be convenient for researchers to conduct further research on protein interactions.
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Affiliation(s)
- Yuyao Yan
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.
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8
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Henikoff S, Ahmad K. In situ tools for chromatin structural epigenomics. Protein Sci 2022; 31:e4458. [PMID: 36170035 PMCID: PMC9601787 DOI: 10.1002/pro.4458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
Technological progress over the past 15 years has fueled an explosion in genome-wide chromatin profiling tools that take advantage of low-cost short-read sequencing technologies to map particular chromatin features. Here, we survey the recent development of epigenomic tools that provide precise positions of chromatin proteins genome-wide in intact cells or nuclei. Some profiling tools are based on tethering Micrococcal Nuclease to chromatin proteins of interest in situ, whereas others similarly tether Tn5 transposase to integrate DNA sequencing adapters (tagmentation) and so eliminate the need for library preparation. These in situ cleavage and tagmentation tools have gained in popularity over the past few years, with many protocol enhancements and adaptations for single-cell and spatial chromatin profiling. The application of experimental and computational tools to address problems in gene regulation, eukaryotic development, and human disease are helping to define the emerging field of chromatin structural epigenomics.
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Affiliation(s)
- Steven Henikoff
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Kami Ahmad
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
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9
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Xu S, Liu Y, Miao J. Chromatin Immunoprecipitation Assay in Primary Mouse Hepatocytes and Mouse Liver. Methods Mol Biol 2022; 2455:149-161. [PMID: 35212993 PMCID: PMC9642072 DOI: 10.1007/978-1-0716-2128-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Non-alcoholic steatohepatitis (NASH) is an advanced form of non-alcoholic fatty liver disease characterized by hepatosteatosis, liver cell injury, and inflammation. The pathogenesis of NASH involves dysregulated transcription of genes involved in critical processes in the liver, including metabolic homeostasis and inflammation. Chromatin immunoprecipitation (ChIP) utilizes antibody-mediated immunoprecipitation followed by the detection of associated DNA fragments via real-time PCR or high-throughput sequencing to quantitatively profile the interactions of proteins of interest with functional chromatin elements. Here, we present a detailed protocol to study the interactions of DNA and chromatin-associated proteins (e.g., transcription factors, co-activators, co-repressors, and chromatin modifiers) and modified histones (e.g., acetylated and methylated) in isolated primary mouse hepatocytes and mouse liver. The application of these methods can enable the identification of molecular mechanisms that underpin dysregulated hepatic processes in NASH.
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Affiliation(s)
- Simiao Xu
- Division of Endocrinology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Branch of the National Clinical Research Center for Metabolic Disease, Wuhan, China
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yangyang Liu
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ji Miao
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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10
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Ferraz RAC, Lopes ALG, da Silva JAF, Moreira DFV, Ferreira MJN, de Almeida Coimbra SV. DNA-protein interaction studies: a historical and comparative analysis. PLANT METHODS 2021; 17:82. [PMID: 34301293 PMCID: PMC8299673 DOI: 10.1186/s13007-021-00780-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/11/2021] [Indexed: 05/05/2023]
Abstract
DNA-protein interactions are essential for several molecular and cellular mechanisms, such as transcription, transcriptional regulation, DNA modifications, among others. For many decades scientists tried to unravel how DNA links to proteins, forming complex and vital interactions. However, the high number of techniques developed for the study of these interactions made the choice of the appropriate technique a difficult task. This review intends to provide a historical context and compile the methods that describe DNA-protein interactions according to the purpose of each approach, summarise the respective advantages and disadvantages and give some examples of recent uses for each technique. The final aim of this work is to help in deciding which technique to perform according to the objectives and capacities of each research team. Considering the DNA-binding proteins characterisation, filter binding assay and EMSA are easy in vitro methods that rapidly identify nucleic acid-protein binding interactions. To find DNA-binding sites, DNA-footprinting is indeed an easier, faster and reliable approach, however, techniques involving base analogues and base-site selection are more precise. Concerning binding kinetics and affinities, filter binding assay and EMSA are useful and easy methods, although SPR and spectroscopy techniques are more sensitive. Finally, relatively to genome-wide studies, ChIP-seq is the desired method, given the coverage and resolution of the technique. In conclusion, although some experiments are easier and faster than others, when designing a DNA-protein interaction study several concerns should be taken and different techniques may need to be considered, since different methods confer different precisions and accuracies.
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Affiliation(s)
- Ricardo André Campos Ferraz
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Ana Lúcia Gonçalves Lopes
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Jessy Ariana Faria da Silva
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
- Universidade do Minho, Braga, Portugal
| | - Diana Filipa Viana Moreira
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Maria João Nogueira Ferreira
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Sílvia Vieira de Almeida Coimbra
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal.
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11
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Sen I, Kavšek A, Riedel CG. Chromatin Immunoprecipitation and Sequencing (ChIP-seq) Optimized for Application in Caenorhabditis elegans. Curr Protoc 2021; 1:e187. [PMID: 34242493 DOI: 10.1002/cpz1.187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) has become one of the most popular methods to study protein-DNA interactions and can be used, for instance, to identify the binding sites of transcription factors or to determine the distributions of histones with specific post-translational modifications throughout the genome. Although standard ChIP-seq protocols work well in most experimental systems, there are exceptions, and one of these is the popular model organism Caenorhabditis elegans. Even though this system is very amenable to genetic and cytological methods, biochemical approaches are challenging. This is due to both the animals' cuticle, which impairs lysis as well as penetration by cross-linkers, and the rather low protein and chromatin content per body weight. These issues have rendered standard ChIP-seq protocols inefficient in C. elegans and raised a need for their improvement. Here, we describe improved protocols, with the most important advances being the efficient breakage of the C. elegans cuticle by freeze-grinding and the use of a very sensitive sequencing library construction procedure, optimized for the relatively low DNA content per body weight of C. elegans. The protocols should therefore improve the reproducibility, sensitivity, and uniformity across tissues of ChIP-seq in this organism. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Growth and harvesting of synchronized Caenorhabditis elegans Basic Protocol 2: Chromatin immunoprecipitation (ChIP) Basic Protocol 3: Library construction for Illumina sequencing.
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Affiliation(s)
- Ilke Sen
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Alan Kavšek
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Christian G Riedel
- Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
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12
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Patty BJ, Hainer SJ. Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts. Nat Protoc 2021; 16:2633-2666. [PMID: 33911257 PMCID: PMC8177051 DOI: 10.1038/s41596-021-00516-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/04/2021] [Indexed: 02/02/2023]
Abstract
Determining chromatin-associated protein localization across the genome has provided insight into the functions of DNA-binding proteins and their connections to disease. However, established protocols requiring large quantities of cell or tissue samples currently limit applications for clinical and biomedical research in this field. Furthermore, most technologies have been optimized to assess abundant histone protein localization, prohibiting the investigation of nonhistone protein localization in low cell numbers. We recently described a protocol to profile chromatin-associated protein localization in as low as one cell: ultra-low-input cleavage under targets and release using nuclease (uliCUT&RUN). Optimized from chromatin immunocleavage and CUT&RUN, uliCUT&RUN is a tethered enzyme-based protocol that utilizes a combination of recombinant protein, antibody recognition and stringent purification to selectively target proteins of interest and isolate the associated DNA. Performed in native conditions, uliCUT&RUN profiles protein localization to chromatin with low input and high precision. Compared with other profiling technologies, uliCUT&RUN can determine nonhistone protein chromatin occupancies in low cell numbers, permitting the investigation into the molecular functions of a range of DNA-binding proteins within rare samples. From sample preparation to sequencing library submission, the uliCUT&RUN protocol takes <2 d to perform, with the accompanying data analysis timeline dependent on experience level.
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Affiliation(s)
- Benjamin J Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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13
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Chromatin Immunoprecipitation (ChIP) to Study DNA-Protein Interactions. Methods Mol Biol 2021. [PMID: 33420999 DOI: 10.1007/978-1-0716-1186-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Chromatin immunoprecipitation (ChIP) is a method used to examine the genomic localization of a target of interest (e.g., proteins, protein posttranslational modifications, or DNA elements). As ChIP provides a snapshot of in vivo DNA-protein interactions, it lends insight to the mechanisms of gene expression and genome regulation. This chapter provides a detailed protocol focused on native-ChIP (N-ChIP), a robust approach to profile stable DNA-protein interactions. We also describe best practices for ChIP , including defined controls to ensure specific and efficient target enrichment and methods for data normalization.
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14
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Kerdivel G, Boeva V. Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-Seq) Analysis in Ewing Sarcoma. Methods Mol Biol 2021; 2226:265-284. [PMID: 33326109 DOI: 10.1007/978-1-0716-1020-6_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ChIP-seq is the method of choice for profiling protein-DNA interactions, and notably for characterizing the landscape of transcription factor binding and histone modifications. This technique has been widely used to study numerous aspects of tumor biology and led to the development of several promising cancer therapies. In Ewing sarcoma research, ChIP-seq provided important insights into the mechanism of action of the major oncogenic fusion protein EWSR1-FLI1 and related epigenetic and transcriptional changes. In this chapter, we provide a detailed pipeline to analyze ChIP-seq experiments from the preprocessing of raw data to tertiary analysis of detected binding sites. We also advise on best practice to prepare tumor samples prior to sequencing.
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Affiliation(s)
- Gwenneg Kerdivel
- Cochin Institute, INSERM U1016, CNRS UMR8104, University of Paris, Paris, France.
| | - Valentina Boeva
- INSERM, U1016, Cochin Institute, CNRS UMR8104, Paris Descartes University, Paris, France. .,Department of Computer Science, ETH Zurich, Institute for Machine Learning, Zurich, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Zürich, Switzerland.
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15
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Abstract
Tumor immunology is undergoing a renaissance due to the recent profound clinical successes of tumor immunotherapy. These advances have coincided with an exponential growth in the development of -omics technologies. Armed with these technologies and their associated computational and modeling toolsets, systems biologists have turned their attention to tumor immunology in an effort to understand the precise nature and consequences of interactions between tumors and the immune system. Such interactions are inherently multivariate, spanning multiple time and size scales, cell types, and organ systems, rendering systems biology approaches particularly amenable to their interrogation. While in its infancy, the field of 'Cancer Systems Immunology' has already influenced our understanding of tumor immunology and immunotherapy. As the field matures, studies will move beyond descriptive characterizations toward functional investigations of the emergent behavior that govern tumor-immune responses. Thus, Cancer Systems Immunology holds incredible promise to advance our ability to fight this disease.
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Affiliation(s)
| | - Edgar G Engleman
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of MedicineStanfordUnited States
- Stanford Cancer Institute, Stanford UniversityStanfordUnited States
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16
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Lloyd SM, Bao X. Pinpointing the Genomic Localizations of Chromatin-Associated Proteins: The Yesterday, Today, and Tomorrow of ChIP-seq. ACTA ACUST UNITED AC 2020; 84:e89. [PMID: 31483109 DOI: 10.1002/cpcb.89] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chromatin-associated proteins are instrumental for controlling spatiotemporal gene expression. Determining where these proteins bind across the genome is critical for understanding gene regulation. A widely used technique at present is ChIP-seq, which leverages chromatin fragmentation, antibody-mediated enrichment, next-generation sequencing, and data analysis to uncover the genomic sequences and patterns of protein-DNA interactions. In this article, we will provide an overview of how ChIP-seq was developed, the key elements of the experimentation and data analysis pipeline, and the recent variations that push the boundaries of precision and cell number requirements. We will also briefly discuss how future development of ChIP-seq may further advance our understanding of chromatin biology. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sarah M Lloyd
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois
| | - Xiaomin Bao
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois.,Department of Dermatology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois
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17
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Chromatin Immunoprecipitation from Caenorhabditis elegans Somatic Cells. Methods Mol Biol 2020. [PMID: 32410034 DOI: 10.1007/978-1-0716-0592-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Chromatin Immunoprecipitation is a regularly used method to detect DNA-protein interaction in diverse biological samples. Here we describe the application of ChIP for histone modifications in adult-stage Caenorhabditis elegans somatic cells.
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18
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Hamamoto R, Komatsu M, Takasawa K, Asada K, Kaneko S. Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine. Biomolecules 2019; 10:biom10010062. [PMID: 31905969 PMCID: PMC7023005 DOI: 10.3390/biom10010062] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/20/2019] [Accepted: 12/27/2019] [Indexed: 12/14/2022] Open
Abstract
To clarify the mechanisms of diseases, such as cancer, studies analyzing genetic mutations have been actively conducted for a long time, and a large number of achievements have already been reported. Indeed, genomic medicine is considered the core discipline of precision medicine, and currently, the clinical application of cutting-edge genomic medicine aimed at improving the prevention, diagnosis and treatment of a wide range of diseases is promoted. However, although the Human Genome Project was completed in 2003 and large-scale genetic analyses have since been accomplished worldwide with the development of next-generation sequencing (NGS), explaining the mechanism of disease onset only using genetic variation has been recognized as difficult. Meanwhile, the importance of epigenetics, which describes inheritance by mechanisms other than the genomic DNA sequence, has recently attracted attention, and, in particular, many studies have reported the involvement of epigenetic deregulation in human cancer. So far, given that genetic and epigenetic studies tend to be accomplished independently, physiological relationships between genetics and epigenetics in diseases remain almost unknown. Since this situation may be a disadvantage to developing precision medicine, the integrated understanding of genetic variation and epigenetic deregulation appears to be now critical. Importantly, the current progress of artificial intelligence (AI) technologies, such as machine learning and deep learning, is remarkable and enables multimodal analyses of big omics data. In this regard, it is important to develop a platform that can conduct multimodal analysis of medical big data using AI as this may accelerate the realization of precision medicine. In this review, we discuss the importance of genome-wide epigenetic and multiomics analyses using AI in the era of precision medicine.
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Affiliation(s)
- Ryuji Hamamoto
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
- Correspondence: ; Tel.: +81-3-3547-5271
| | - Masaaki Komatsu
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Ken Takasawa
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Ken Asada
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (M.K.); (K.T.); (K.A.); (S.K.)
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19
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Simon MD, Machyna M. Principles and Practices of Hybridization Capture Experiments to Study Long Noncoding RNAs That Act on Chromatin. Cold Spring Harb Perspect Biol 2019; 11:11/11/a032276. [PMID: 31676573 DOI: 10.1101/cshperspect.a032276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The diverse roles of cellular RNAs can be studied by purifying RNAs of interest together with the biomolecules they bind. Biotinylated antisense oligonucleotides that hybridize specifically to the RNA of interest provide a general approach to develop affinity reagents for these experiments. Such oligonucleotides can be used to enrich endogenous RNAs from cross-linked chromatin extracts to study the genomic binding sites of RNAs. These hybridization capture protocols are evolving modular experiments that are compatible with a range of cross-linkers and conditions. This review discusses the principles of these hybridization capture experiments as well as considerations and controls necessary to interpret the resulting data without being misled by artifactual signals.
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Affiliation(s)
- Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Martin Machyna
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
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20
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Hainer SJ, Fazzio TG. High-Resolution Chromatin Profiling Using CUT&RUN. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2019; 126:e85. [PMID: 30688406 PMCID: PMC6422702 DOI: 10.1002/cpmb.85] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Determining the genomic location of DNA-binding proteins is essential to understanding their function. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a powerful method for mapping protein-DNA interactions at high resolution. In CUT&RUN, a recombinant protein A-microccocal nuclease (pA-MN) fusion is recruited by an antibody targeting the chromatin protein of interest; this can be done with either uncrosslinked or formaldehyde-crosslinked cells. DNA fragments near sites of antibody binding are released from the insoluble bulk chromatin through endonucleolytic cleavage and used to build barcoded DNA-sequencing libraries that can be sequenced in pools of at least 30. Therefore, CUT&RUN provides an alternative to ChIP-seq approaches for mapping chromatin proteins, which typically have relatively high signal-to-noise ratios, while using fewer cells and at a lower cost. Here, we describe the methods for performing CUT&RUN, generating DNA-sequencing libraries, and analyzing the resulting datasets. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Thomas G. Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01604, USA
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21
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Emamjomeh A, Choobineh D, Hajieghrari B, MahdiNezhad N, Khodavirdipour A. DNA-protein interaction: identification, prediction and data analysis. Mol Biol Rep 2019; 46:3571-3596. [PMID: 30915687 DOI: 10.1007/s11033-019-04763-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022]
Abstract
Life in living organisms is dependent on specific and purposeful interaction between other molecules. Such purposeful interactions make the various processes inside the cells and the bodies of living organisms possible. DNA-protein interactions, among all the types of interactions between different molecules, are of considerable importance. Currently, with the development of numerous experimental techniques, diverse methods are convenient for recognition and investigating such interactions. While the traditional experimental techniques to identify DNA-protein complexes are time-consuming and are unsuitable for genome-scale studies, the current high throughput approaches are more efficient in determining such interaction at a large-scale, but they are clearly too costly to be practice for daily applications. Hence, according to the availability of much information related to different biological sequences and clearing different dimensions of conditions in which such interactions are formed, with the developments related to the computer, mathematics, and statistics motivate scientists to develop bioinformatics tools for prediction the interaction site(s). Until now, there has been much progress in this field. In this review, the factors and conditions governing the interaction and the laboratory techniques for examining such interactions are addressed. In addition, developed bioinformatics tools are introduced and compared for this reason and, in the end, several suggestions are offered for the promotion of such tools in prediction with much more precision.
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Affiliation(s)
- Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, 98615-538, Iran.
| | - Darush Choobineh
- Agricultural Biotechnology, Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, 74135-111, Iran.
| | - Nafiseh MahdiNezhad
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, 98615-538, Iran
| | - Amir Khodavirdipour
- Division of Human Genetics, Department of Anatomy, St. John's hospital, Bangalore, India
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22
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Policastro RA, Zentner GE. Enzymatic methods for genome-wide profiling of protein binding sites. Brief Funct Genomics 2019; 17:138-145. [PMID: 29028882 DOI: 10.1093/bfgp/elx030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Genome-wide mapping of protein-DNA interactions is a staple approach in many areas of modern molecular biology. Genome-wide profiles of protein-binding sites are most commonly generated by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). Although ChIP-seq has played a central role in studying genome-wide protein binding, recent work has highlighted systematic biases in the technique that warrant technical and interpretive caution and underscore the need for orthogonal techniques to both confirm the results of ChIP-seq studies and uncover new insights not accessible to ChIP. Several such techniques, based on genetic or immunological targeting of enzymatic activity to specific genomic loci, have been developed. Here, we review the development, applications and future prospects of these methods as complements to ChIP-based approaches and as powerful techniques in their own right.
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23
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Venters BJ. Insights from resolving protein-DNA interactions at near base-pair resolution. Brief Funct Genomics 2019; 17:80-88. [PMID: 29211822 DOI: 10.1093/bfgp/elx043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One of the central goals in molecular biology is to understand how cell-type-specific expression patterns arise through selective recruitment of RNA polymerase II (Pol II) to a subset of gene promoters. Pol II needs to be recruited to a precise genomic position at the proper time to produce messenger RNA from a DNA template. Ostensibly, transcription is a relatively simple cellular process; yet, experimentally measuring and then understanding the combinatorial possibilities of transcriptional regulators remain a daunting task. Since its introduction in 1985, chromatin immunoprecipitation (ChIP) has remained a key tool for investigating protein-DNA contacts in vivo. Over 30 years of intensive research using ChIP have provided numerous insights into mechanisms of gene regulation. As functional genomic technologies improve, they present new opportunities to address key biological questions. ChIP-exo is a refined version of ChIP-seq that significantly reduces background signal, while providing near base-pair mapping resolution for protein-DNA interactions. This review discusses the evolution of the ChIP assay over the years; the methodological differences between ChIP-seq, ChIP-exo and ChIP-nexus; and highlight new insights into epigenetic and transcriptional mechanisms that were uniquely enabled with the near base-pair resolution of ChIP-exo.
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24
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Wang XQD, Cameron CJF, Paquette D, Segal D, Warsaba R, Blanchette M, Dostie J. 2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing. BMC Genomics 2019; 20:162. [PMID: 30819105 PMCID: PMC6394006 DOI: 10.1186/s12864-019-5532-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/15/2019] [Indexed: 11/12/2022] Open
Abstract
Background Understanding how transcription occurs requires the integration of genome-wide and locus-specific information gleaned from robust technologies. Chromatin immunoprecipitation (ChIP) is a staple in gene expression studies, and while genome-wide methods are available, high-throughput approaches to analyze defined regions are lacking. Results Here, we present carbon copy-ChIP (2C-ChIP), a versatile, inexpensive, and high-throughput technique to quantitatively measure the abundance of DNA sequences in ChIP samples. This method combines ChIP with ligation-mediated amplification (LMA) and deep sequencing to probe large genomic regions of interest. 2C-ChIP recapitulates results from benchmark ChIP approaches. We applied 2C-ChIP to the HOXA cluster to find that a region where H3K27me3 and SUZ12 linger encodes HOXA-AS2, a long non-coding RNA that enhances gene expression during cellular differentiation. Conclusions 2C-ChIP fills the need for a robust molecular biology tool designed to probe dedicated genomic regions in a high-throughput setting. The flexible nature of the 2C-ChIP approach allows rapid changes in experimental design at relatively low cost, making it a highly efficient method for chromatin analysis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5532-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xue Qing David Wang
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Christopher J F Cameron
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada.,School of Computer Science and McGill Center for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Denis Paquette
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Dana Segal
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Reid Warsaba
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Mathieu Blanchette
- School of Computer Science and McGill Center for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada
| | - Josée Dostie
- Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada.
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25
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Wolfe KB, Long DT. Chromatin Immunoprecipitation (ChIP) of Plasmid-Bound Proteins in Xenopus Egg Extracts. Methods Mol Biol 2019; 1999:173-184. [PMID: 31127576 PMCID: PMC8091904 DOI: 10.1007/978-1-4939-9500-4_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Xenopus egg extracts provide a cell-free system to analyze various aspects of chromatin biology. Here we describe a modified method of chromatin immunoprecipitation (ChIP) to detect the interaction of proteins with plasmid DNA incubated in extract. The combination of ChIP and Xenopus egg extracts provides a highly versatile and tractable approach to analyze dynamic protein-DNA interactions with great spatial and temporal detail.
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Affiliation(s)
- Kelly B Wolfe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - David T Long
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA.
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26
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Sun D. Chromatin Immunoprecipitation Assay to Analyze the Effect of G-Quadruplex Interactive Agents on the Binding of RNA Polymerase II and Transcription Factors to a Target Promoter Region. Methods Mol Biol 2019; 2035:233-242. [PMID: 31444753 DOI: 10.1007/978-1-4939-9666-7_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Growing evidence suggests the existence of G-quadruplexes and their involvement in transcriptional regulation of many human genes, including VEGF. These studies also provide strong evidence that G-quadruplex structures are stabilized by binding to small molecules, resulting in the modulation of the transcription of genes whose promoters form G-quadruplexes. Here, we describe a chromatin immunoprecipitation (ChIP) assay to determine whether G-quadruplex-interactive agents influence the recruitment of cellular transcription factors, such as Sp1, nucleolin, or hnRNP-K to target genes that contain potential G-quadruplex (G4)-forming sequences in their promoters, subsequently modulating the occupancy of RNA Pol II on the same promoter region.
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Affiliation(s)
- Daekyu Sun
- College of Pharmacy, University of Arizona, Tucson, AZ, USA.
- BIO5 Institute, Tucson, AZ, USA.
- Arizona Cancer Center, Tucson, AZ, USA.
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27
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Abstract
Transposable elements (TEs) are low-complexity elements (e.g., LINEs, SINEs, SVAs, and HERVs) that make up to two-thirds of the human genome. There is mounting evidence that TEs play an essential role in molecular functions that influence genomic plasticity and gene expression regulation. With the advent of next-generation sequencing approaches, our understanding of the relationship between TEs and psychiatric disorders will greatly improve. In this chapter, the Authors comprehensively summarize the state-of the-art of TE research in animal models and humans supporting a framework in which TEs play a functional role in mechanisms affecting a variety of behaviors, including neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Finally, the Authors discuss recent therapeutic applications raised from the increasing experimental evidence on TE functional mechanisms.
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Affiliation(s)
- G Guffanti
- McLean Hospital - Harvard Medical School, Belmont, MA, USA.
| | - A Bartlett
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
| | - P DeCrescenzo
- McLean Hospital - Harvard Medical School, Belmont, MA, USA
| | - F Macciardi
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA
| | - R Hunter
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
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28
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Murarka P, Srivastava P. An improved method for the isolation and identification of unknown proteins that bind to known DNA sequences by affinity capture and mass spectrometry. PLoS One 2018; 13:e0202602. [PMID: 30138440 PMCID: PMC6107227 DOI: 10.1371/journal.pone.0202602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 08/05/2018] [Indexed: 12/13/2022] Open
Abstract
Transcription of a gene can be regulated at many different levels. One such fundamental level is interaction between protein and DNA. Protein(s) binds to distinct sites on the DNA, which activate, enhance or repress transcription. Despite being such an important process, very few tools exist to identify the proteins that interact with chromosome, most of which are in vitro in nature. Here, we propose an in vivo based method for identification of DNA binding protein(s) in bacteria where the DNA-protein complex formed in vivo is crosslinked by formaldehyde. This complex is further isolated and the bound proteins are identified. The method was used to isolate promoter DNA binding proteins, which bind and regulate the dsz operon in Gordonia sp. IITR 100 responsible for biodesulfurization of organosulfurs. The promoter binding proteins were identified by MALDI ToF MS/MS and the binding was confirmed by gel shift assay. Unlike other reported in vivo methods, this improved method does not require sequence of the whole genome or a chip and can be scaled up to improve yields.
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Affiliation(s)
- Pooja Murarka
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
- * E-mail: ,
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29
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Raje HS, Lieux ME, DiMario PJ. R1 retrotransposons in the nucleolar organizers of Drosophila melanogaster are transcribed by RNA polymerase I upon heat shock. Transcription 2018; 9:273-285. [PMID: 30063880 DOI: 10.1080/21541264.2018.1506682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The ribosomal RNA genes (rDNA) of Drosophila melanogaster reside within centromere-proximal nucleolar organizers on both the X and Y chromosomes. Each locus contains between 200-300 tandem repeat rDNA units that encode 18S, 5.8S, 2S, and 28S ribosomal RNAs (rRNAs) necessary for ribosome biogenesis. In arthropods like Drosophila, about 60% of the rDNA genes have R1 and/or R2 retrotransposons inserted at specific sites within their 28S regions; these units likely fail to produce functional 28S rRNA. We showed earlier that R2 expression increases upon nucleolar stress caused by the loss of the ribosome assembly factor, Nucleolar Phosphoprotein of 140 kDa (Nopp140). Here we show that R1 expression is selectively induced by heat shock. Actinomycin D, but not α-amanitin, blocked R1 expression in S2 cells upon heat shock, indicating that R1 elements are transcribed by Pol I. A series of RT-PCRs established read-through transcription by Pol I from the 28S gene region into R1. Sequencing the RT-PCR products confirmed the 28S-R1 RNA junction and the expression of R1 elements within nucleolar rDNA rather than R1 elements known to reside in centromeric heterochromatin. Using a genome-wide precision run-on sequencing (PRO-seq) data set available at NCBI-GEO, we show that Pol I activity on R1 elements is negligible under normal non-heat shock conditions but increases upon heat shock. We propose that prior to heat shock Pol I pauses within the 5' end of R1 where we find a consensus "pause button", and that heat shock releases Pol I for read-through transcription farther into R1.
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Affiliation(s)
- Himanshu S Raje
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Molly E Lieux
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Patrick J DiMario
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
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30
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Abstract
Chromatin immunoprecipitation (ChIP) is a powerful method used for identifying genome-wide DNA-protein interactions in vivo. A large number of essential intracellular processes such as DNA replication, transcription regulation, chromatin stability, and others are all dependent on protein interactions with DNA. The DNA fragments enriched from the ChIP assay are analyzed by downstream applications, for example, microarray hybridization (ChIP-chip), quantitative PCR (ChIP-qPCR), or deep sequencing (ChIP-seq). This chapter presents a stepwise protocol for ChIP performed in hyperthermophilic archaea that we have successfully used in the hyperthermoacidophilic crenarchaeon Sulfolobus acidocaldarius.
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31
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Clark RF, Cho KW, Weinmann R, Hamkalo BA. Preferential distribution of active RNA polymerase II molecules in the nuclear periphery. Gene Expr 2018; 1:61-70. [PMID: 1668144 PMCID: PMC5952200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have combined immunogold labeling with the Miller spreading technique in order to localize proteins at the electron microscope (EM) level in whole mount nuclei from mouse and human fibroblasts. Anti-histone H1 antibody labels nuclei uniformly, indicating that the nuclear interior is accessible to both antibodies and gold conjugates. Anti-topoisomerase I antibody labels nucleoli intensely, in agreement with previous immunofluorescent and biochemical data. Two different antibodies against the large subunit of RNA polymerase II (pol II) show preferential labeling of the nuclear periphery, as do antibodies against lamin, a known peripheral nuclear protein. Treatment of cells with alpha-amanitin results in loss of virtually all RNA polymerase II staining, supporting the specificity of labeling. Finally, when nuclei are incubated in the presence of biotin-UTP (bio-UTP) under run-off transcription conditions, incorporation is preferentially located at the nuclear periphery. These results support the conclusions that transcriptionally active pol II molecules are non-uniformly distributed in fibroblast nuclei, and that their differential distribution mirrors that of total pol II.
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Affiliation(s)
- R F Clark
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92717
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32
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Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies. Methods 2018; 144:64-78. [PMID: 29753003 DOI: 10.1016/j.ymeth.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
With the goal of expanding the very limited toolkit of cross-linking agents available for nucleic acids and their protein complexes, we evaluated the merits of a wide range of bifunctional agents that may be capable of reacting with the functional groups characteristic of these types of biopolymers. The survey specifically focused on the ability of test reagents to produce desirable inter-molecular conjugates, which could reveal the identity of interacting components and the position of mutual contacts, while also considering a series of practical criteria for their utilization as viable nucleic acid probes. The survey employed models consisting of DNA, RNA, and corresponding protein complexes to mimic as close as possible typical applications. Denaturing polyacrylamide gel electrophoresis (PAGE) and mass spectrometric (MS) analyses were implemented in concert to monitor the formation of the desired conjugates. In particular, the former was used as a rapid and inexpensive tool for the efficient evaluation of cross-linker activity under a broad range of experimental conditions. The latter was applied after preliminary rounds of reaction optimization to enable full-fledged product characterization and, more significantly, differentiation between mono-functional and intra- versus inter-molecular conjugates. This information provided the feedback necessary to further optimize reaction conditions and explain possible outcomes. Among the reagents tested in the study, platinum complexes and nitrogen mustards manifested the most favorable characteristics for practical cross-linking applications, whereas other compounds provided inferior yields, or produced rather unstable conjugates that did not survive the selected analytical conditions. The observed outcomes will help guide the selection of the most appropriate cross-linking reagent for a specific task, whereas the experimental conditions described here will provide an excellent starting point for approaching these types of applications. As a whole, the results of the survey clearly emphasize that finding a universal reagent, which may afford excellent performance with all types of nucleic acid substrates, will require extending the exploration beyond the traditional chemistries employed to modify the constitutive functional groups of these vital biopolymers.
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33
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Marinov GK, Kundaje A. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. Brief Funct Genomics 2018; 17:116-137. [PMID: 29529131 PMCID: PMC5889016 DOI: 10.1093/bfgp/ely004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Advances in the methods for detecting protein-DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput sequencing (ChIP-seq) as a readout for ChIP assays. In addition to the numerous other ways in which it is superior to arrays, by eliminating the need to design and manufacture them, sequencing also opened the door to carrying out comparative analyses of genome-wide transcription factor occupancy across species and studying chromatin biology in previously less accessible model and nonmodel organisms, thus allowing us to understand the evolution and diversity of regulatory mechanisms in unprecedented detail. Here, we review the biological insights obtained from such studies in recent years and discuss anticipated future developments in the field.
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Affiliation(s)
- Georgi K Marinov
- Corresponding author: Georgi K. Marinov, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. E-mail:
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34
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Chromatin Immunoprecipitation of HIF-α in Breast Tumor Cells Using Wild Type and Loss of Function Models. Methods Mol Biol 2018. [PMID: 29330791 DOI: 10.1007/978-1-4939-7665-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Chromatin immunoprecipitation (ChIP) is a powerful method to determine whether a protein of interest binds to specific regulatory elements of the genome. Herein, we outline protocols optimized to detect binding of Hypoxia-Inducible Factor (HIF)-1α or HIF-2α to putative hypoxia response elements (HREs) within HIF target genes expressed in breast tumor epithelial cells.
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35
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Löser E, Latreille D, Iovino N. Chromatin Preparation and Chromatin Immuno-precipitation from Drosophila Embryos. Methods Mol Biol 2018; 1480:23-36. [PMID: 27659972 DOI: 10.1007/978-1-4939-6380-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
This protocol provides specific details on how to perform Chromatin immunoprecipitation (ChIP) from Drosophila embryos. ChIP allows the matching of proteins or histone modifications to specific genomic regions. Formaldehyde-cross-linked chromatin is isolated and antibodies against the target of interest are used to determine whether the target is associated with a specific DNA sequence. This can be performed in spatial and temporal manner and it can provide information about the genome-wide localization of a given protein or histone modification if coupled with deep sequencing technology (ChIP-Seq).
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Affiliation(s)
- Eva Löser
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
| | - Daniel Latreille
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
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36
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Lee M, Gudas LJ, Saavedra HI. Detection of E2F-DNA Complexes Using Chromatin Immunoprecipitation Assays. Methods Mol Biol 2018; 1726:143-151. [PMID: 29468550 PMCID: PMC6070307 DOI: 10.1007/978-1-4939-7565-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chromatin immunoprecipitation (ChIP), originally developed by John T. Lis and David Gilmour in 1984, has been useful to detect DNA sequences where protein(s) of interest bind. ChIP is comprised of several steps: (1) cross-linking of proteins to target DNA sequences, (2) breaking genomic DNA into 300-1000 bp pieces by sonication or nuclease digestion, (3) immunoprecipitation of protein bound to target DNA with an antibody, (4) reverse cross-linking between target DNA and the bound protein to liberate the DNA fragments, and (5) amplification of target DNA fragment by PCR. Since then, the technology has evolved significantly to allow not only amplifying target sequences by PCR, but also sequencing all DNA fragment bound to a target protein, using a variant of the approach called the ChIP-seq technique (1). Another variation, the ChIP-on-ChIP, allows the detection of protein complexes bound to specific DNA sequences (2).
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Affiliation(s)
- Miyoung Lee
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Medical College of Cornell University, New York, NY, USA
| | - Harold I Saavedra
- Pharmacology Division, Department of Basic Sciences, Ponce Health Sciences University, Ponce, Puerto Rico.
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37
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Abstract
Chromatin immunoprecipitation paired with next-generation sequencing (ChIP-seq) can be used to determine genome-wide distribution of transcriptions factors, transcriptional machinery, or histone modifications. DNA-protein interactions are covalently cross-linked with the addition of formaldehyde. Chromatin is prepared and sheared, then immunoprecipitated with the appropriate antibody. After reversal of cross-linking and treating with protease, the resulting DNA fragments are sequenced and mapped to the reference genome to determine overall enrichment. Here we describe a method of ChIP-seq for investigating protein-DNA interactions in the filamentous fungus Neurospora crassa.
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Affiliation(s)
- Aileen R Ferraro
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Zachary A Lewis
- Department of Microbiology, University of Georgia, Athens, GA, USA.
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38
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ChIP and ChIP-Related Techniques: Expanding the Fields of Application and Improving ChIP Performance. Methods Mol Biol 2018; 1689:1-7. [PMID: 29027160 DOI: 10.1007/978-1-4939-7380-4_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein-DNA interactions in vivo can be detected and quantified by chromatin immunoprecipitation (ChIP). ChIP has been instrumental for the advancement of epigenetics and has set the groundwork for the development of a number of ChIP-related techniques that have provided valuable information about the organization and function of genomes. Here, we provide an introduction to ChIP and discuss the applications of ChIP in different research areas. We also review some of the strategies that have been devised to improve ChIP performance.
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39
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Jordán-Pla A, Visa N. Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments. Methods Mol Biol 2018; 1689:9-28. [PMID: 29027161 DOI: 10.1007/978-1-4939-7380-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation.In this chapter, we provide a general overview of the ChIP method and its most common variations, with a special focus on ChIP-seq. We try to address some of the most important aspects that need to be taken into account in order to design and perform experiments that generate the most reproducible, high-quality data. Some of the main topics covered include the use of properly characterized antibodies, alternatives to chromatin preparation, the need for proper controls, and some recommendations about ChIP-seq data analysis.
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Affiliation(s)
- Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20c, 10691, Stockholm, Sweden.
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20c, 10691, Stockholm, Sweden
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40
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Estalayo-Adrián S, Garnir K, Moucheron C. Perspectives of ruthenium(ii) polyazaaromatic photo-oxidizing complexes photoreactive towards tryptophan-containing peptides and derivatives. Chem Commun (Camb) 2018; 54:322-337. [DOI: 10.1039/c7cc06542f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This review focuses on recent advances in the search for RuII polyazaaromatic complexes as molecular photoreagents for tryptophan-containing peptides and proteins, in view of future biomedical applications.
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Affiliation(s)
- S. Estalayo-Adrián
- Organic Chemistry and Photochemistry
- Université Libre de Bruxelles, (U. L. B.)
- 1050 Bruxelles
- Belgium
| | - K. Garnir
- Organic Chemistry and Photochemistry
- Université Libre de Bruxelles, (U. L. B.)
- 1050 Bruxelles
- Belgium
| | - C. Moucheron
- Organic Chemistry and Photochemistry
- Université Libre de Bruxelles, (U. L. B.)
- 1050 Bruxelles
- Belgium
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41
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García-Sánchez A, Marqués-García F. Review of Methods to Study Gene Expression Regulation Applied to Asthma. Methods Mol Biol 2017; 1434:71-89. [PMID: 27300532 DOI: 10.1007/978-1-4939-3652-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Gene expression regulation is the cellular process that controls, increasing or decreasing, the expression of gene products (RNA or protein). A complex set of interactions between genes, RNA molecules, protein, and other components determined when and where specific genes are activated and the amount of protein or RNA produced. Here, we focus on several methods to study gene regulation applied to asthma and allergic research such as: Western Blot to identify and quantify proteins, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) to study protein interactions with nucleic acids, and RNA interference (RNAi) by which gene expression could be silenced.
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Affiliation(s)
- Asunción García-Sánchez
- Department of Biomedical and Diagnostic Sciences, University of Salamanca, Salamanca, Spain. .,Salamanca Institute for Biomedical Research (IBSAL), UniversityHospital of Salamanca, Salamanca, Spain.
| | - Fernando Marqués-García
- Salamanca Institute for Biomedical Research (IBSAL), Salamanca, Spain.,Department of Clinical Biochemistry, University Hospital of Salamanca, Salamanca, Spain
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42
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García-Sánchez A, Marqués-García F. Chromatin Immunoprecipitation: Application to the Study of Asthma. Methods Mol Biol 2017; 1434:121-37. [PMID: 27300535 DOI: 10.1007/978-1-4939-3652-6_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chromatin immunoprecipitation (ChIP) is a technique for studying interactions between proteins and DNA in living cells. A protein of interest is selectively immunoprecipitated from a chromatin preparation, to analyze the DNA sequences involved. ChIP can be used to determine whether a transcription factor interacts with a candidate target gene and to map the localization of histones with posttranslational modifications on the genome.The protein-DNA interactions are captured in vivo by chemical cross-linking. Cell lysis, DNA fragmentation, and immunoaffinity purification of the protein of interest allow to co-purify DNA fragments that are associated with that protein. The enriched protein-DNA population is ready to be quantified by PCR to detect precipitated DNA fragments. The combination of ChIP with DNA microarray analysis (ChIP-on-chip) and high-throughput sequencing (ChIP-seq) has enabled to obtain profiles of transcription factor occupancy sites and histone modifications throughout the genome.
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Affiliation(s)
- Asunción García-Sánchez
- Department of Biomedical and Diagnostic Sciences, University of Salamanca, Salamanca, Spain. .,Salamanca Institute for Biomedical Research (IBSAL), University Hospital of Salamanca, Salamanca, Spain.
| | - Fernándo Marqués-García
- Salamanca Institute for Biomedical Research (IBSAL), Salamanca, Spain.,Department of Clinical Biochemistry, University Hospital of Salamanca, Salamanca, Spain
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43
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King J, Foster J, Davison JM, Rawls JF, Breton G. Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation. Zebrafish 2017; 15:202-205. [PMID: 29173090 DOI: 10.1089/zeb.2017.1486] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The completion of the zebrafish genome sequence and advances in miniaturization and multiplexing were essential to the creation of techniques such as RNA-seq, ChIP-seq, and high-throughput behavioral and chemical screens. Multiplexing was also instrumental in the recent enhancement of the classic yeast one-hybrid interaction techniques to provide unprecedented discovery capabilities for protein-DNA interactions. Unfortunately its use for zebrafish research is currently hampered by the lack of an open reading frame (ORF) clone collection. As a first step toward a complete collection, we describe a small library of transcriptional regulatory proteins comprising 142 ORFs and its potential applications.
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Affiliation(s)
- Justin King
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
| | - Justin Foster
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
| | - James M Davison
- 2 Department of Molecular Genetics and Microbiology, Duke University School of Medicine , Durham, North Carolina
| | - John F Rawls
- 2 Department of Molecular Genetics and Microbiology, Duke University School of Medicine , Durham, North Carolina
| | - Ghislain Breton
- 1 Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston , Houston, Texas
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44
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Steube A, Schenk T, Tretyakov A, Saluz HP. High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells. Nat Commun 2017; 8:1303. [PMID: 29101361 PMCID: PMC5670203 DOI: 10.1038/s41467-017-01251-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 08/31/2017] [Indexed: 01/10/2023] Open
Abstract
Genome-wide mapping of transcription factor binding is generally performed by chemical protein–DNA crosslinking, followed by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Here we present the ChIP-seq technique based on photochemical crosslinking of protein–DNA interactions by high-intensity ultraviolet (UV) laser irradiation in living mammalian cells (UV-ChIP-seq). UV laser irradiation induces an efficient and instant formation of covalent “zero-length” crosslinks exclusively between nucleic acids and proteins that are in immediate contact, thus resulting in a “snapshot” of direct protein–DNA interactions in their natural environment. Here we show that UV-ChIP-seq, applied for genome-wide profiling of the sequence-specific transcriptional repressor B-cell lymphoma 6 (BCL6) in human diffuse large B-cell lymphoma (DLBCL) cells, produces sensitive and precise protein–DNA binding profiles, highly enriched with canonical BCL6 DNA sequence motifs. Using this technique, we also found numerous previously undetectable direct BCL6 binding sites, particularly in condensed, inaccessible areas of chromatin. Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) can map transcription factor binding to a given genome. Here, Steube and colleagues devise a ChIP-seq technique based on photochemical crosslinking by high-intensity ultraviolet laser irradiation, and describe its utility.
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Affiliation(s)
- Arndt Steube
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, 07745, Germany. .,Department of Internal Medicine IV, Jena University Hospital, Friedrich Schiller University, Jena, 07747, Germany. .,Friedrich Schiller University, Jena, 07737, Germany.
| | - Tino Schenk
- Friedrich Schiller University, Jena, 07737, Germany. .,Department of Hematology and Medical Oncology, Clinic of Internal Medicine II, Jena University Hospital, Jena, 07747, Germany. .,Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB), Jena University Hospital, Jena, 07745, Germany.
| | - Alexander Tretyakov
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, 07745, Germany
| | - Hans Peter Saluz
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, 07745, Germany. .,Friedrich Schiller University, Jena, 07737, Germany.
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45
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Long Y, Wang X, Youmans DT, Cech TR. How do lncRNAs regulate transcription? SCIENCE ADVANCES 2017; 3:eaao2110. [PMID: 28959731 PMCID: PMC5617379 DOI: 10.1126/sciadv.aao2110] [Citation(s) in RCA: 466] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/12/2017] [Indexed: 05/11/2023]
Abstract
It has recently become apparent that RNA, itself the product of transcription, is a major regulator of the transcriptional process. In particular, long noncoding RNAs (lncRNAs), which are so numerous in eukaryotes, function in many cases as transcriptional regulators. These RNAs function through binding to histone-modifying complexes, to DNA binding proteins (including transcription factors), and even to RNA polymerase II. In other cases, it is the act of lncRNA transcription rather than the lncRNA product that appears to be regulatory. We review recent progress in elucidating the molecular mechanisms by which lncRNAs modulate gene expression and future opportunities in this research field.
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Affiliation(s)
- Yicheng Long
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Xueyin Wang
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Daniel T. Youmans
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
- Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
| | - Thomas R. Cech
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
- Corresponding author.
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46
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Camborde L, Jauneau A, Brière C, Deslandes L, Dumas B, Gaulin E. Detection of nucleic acid-protein interactions in plant leaves using fluorescence lifetime imaging microscopy. Nat Protoc 2017; 12:1933-1950. [PMID: 28837131 DOI: 10.1038/nprot.2017.076] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA-binding proteins (DNA-BPs) and RNA-binding proteins (RNA-BPs) have critical roles in living cells in all kingdoms of life. Various experimental approaches exist for the study of nucleic acid-protein interactions in vitro and in vivo, but the detection of such interactions at the subcellular level remains challenging. Here we describe how to detect nucleic acid-protein interactions in plant leaves by using a fluorescence resonance energy transfer (FRET) approach coupled to fluorescence lifetime imaging microscopy (FLIM). Proteins of interest (POI) are tagged with a GFP and transiently expressed in plant cells to serve as donor fluorophore. After sample fixation and cell wall permeabilization, leaves are treated with Sytox Orange, a nucleic acid dye that can function as a FRET acceptor. Upon close association of the GFP-tagged POI with Sytox-Orange-stained nucleic acids, a substantial decrease of the GFP lifetime due to FRET between the donor and the acceptor can be monitored. Treatment with RNase before FRET-FLIM measurements allows determination of whether the POI associates with DNA and/or RNA. A step-by-step protocol is provided for sample preparation, data acquisition and analysis. We describe how to calibrate the equipment and include a tutorial explaining the use of the FLIM software. To illustrate our approach, we provide experimental procedures to detect the interaction between plant DNA and two proteins (the AeCRN13 effector from the oomycete Aphanomyces euteiches and the AtWRKY22 defensive transcription factor from Arabidopsis). This protocol allows the detection of protein-nucleic acid interactions in plant cells and can be completed in <2 d.
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Affiliation(s)
- Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS-Université Toulouse, Castanet-Tolosan, France
| | - Alain Jauneau
- CNRS, Plateforme Imagerie-Microscopie, Fédération de Recherche FR3450, Castanet-Tolosan, France
| | - Christian Brière
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS-Université Toulouse, Castanet-Tolosan, France
| | - Laurent Deslandes
- LIPM, Université de Toulouse, INRA, CNRS-Université Toulouse, Castanet-Tolosan, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS-Université Toulouse, Castanet-Tolosan, France
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS-Université Toulouse, Castanet-Tolosan, France
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47
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McCullough SD, On DM, Bowers EC. Using Chromatin Immunoprecipitation in Toxicology: A Step-by-Step Guide to Increasing Efficiency, Reducing Variability, and Expanding Applications. ACTA ACUST UNITED AC 2017; 72:3.14.1-3.14.28. [PMID: 28463415 DOI: 10.1002/cptx.22] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Histone modifications work in concert with DNA methylation to regulate cellular structure, function, and response to environmental stimuli. More than 130 unique histone modifications have been described to date, and chromatin immunoprecipitation (ChIP) allows for the exploration of their associations with the regulatory regions of target genes and other DNA/chromatin-associated proteins across the genome. Many variations of ChIP have been developed in the 30 years since its earliest version came into use, which makes it challenging for users to integrate the procedure into their research programs. Furthermore, the differences in ChIP protocols can confound efforts to increase reproducibility across studies. The streamlined ChIP procedure presented here can be readily applied to samples from a wide range of in vitro studies (cell lines and primary cells) and clinical samples (peripheral leukocytes) in toxicology. We also provide detailed guidance on the optimization of critical protocol parameters, such as chromatin fixation, fragmentation, and immunoprecipitation, to increase efficiency and improve reproducibility. Expanding toxicoepigenetic studies to more readily include histone modifications will facilitate a more comprehensive understanding of the role of the epigenome in environmental exposure effects and the integration of epigenetic data in mechanistic toxicology, adverse outcome pathways, and risk assessment. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Shaun D McCullough
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Doan M On
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina.,Department of Physiology and Biophysics, Medical College of Virginia, Richmond, Virginia
| | - Emma C Bowers
- Curriculum in Toxicology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina
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48
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Ma S, Murphy TW, Lu C. Microfluidics for genome-wide studies involving next generation sequencing. BIOMICROFLUIDICS 2017; 11:021501. [PMID: 28396707 PMCID: PMC5346105 DOI: 10.1063/1.4978426] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/16/2017] [Indexed: 05/11/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized how molecular biology studies are conducted. Its decreasing cost and increasing throughput permit profiling of genomic, transcriptomic, and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this article, we review recent progress on applying microfluidics to facilitate genome-wide studies. We emphasize on several technical aspects of NGS and how they benefit from coupling with microfluidic technology. We also summarize recent efforts on developing microfluidic technology for genomic, transcriptomic, and epigenomic studies, with emphasis on single cell analysis. We envision rapid growth in these directions, driven by the needs for testing scarce primary cell samples from patients in the context of precision medicine.
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Affiliation(s)
- Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech , Blacksburg, Virginia 24061, USA
| | - Travis W Murphy
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
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49
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Hau M, Zenk F, Ganesan A, Iovino N, Jung M. Cellular analysis of the action of epigenetic drugs and probes. Epigenetics 2017; 12:308-322. [PMID: 28071961 DOI: 10.1080/15592294.2016.1274472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Small molecule drugs and probes are important tools in drug discovery, pharmacology, and cell biology. This is of course also true for epigenetic inhibitors. Important examples for the use of established epigenetic inhibitors are the study of the mechanistic role of a certain target in a cellular setting or the modulation of a certain phenotype in an approach that aims toward therapeutic application. Alternatively, cellular testing may aim at the validation of a new epigenetic inhibitor in drug discovery approaches. Cellular and eventually animal models provide powerful tools for these different approaches but certain caveats have to be recognized and taken into account. This involves both the selectivity of the pharmacological tool as well as the specificity and the robustness of the cellular system. In this article, we present an overview of different methods that are used to profile and screen for epigenetic agents and comment on their limitations. We describe not only diverse successful case studies of screening approaches using different assay formats, but also some problematic cases, critically discussing selected applications of these systems.
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Affiliation(s)
- Mirjam Hau
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany
| | - Fides Zenk
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - A Ganesan
- c School of Pharmacy, University of East Anglia , Norwich NR4 7TJ , United Kingdom.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
| | - Nicola Iovino
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - Manfred Jung
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
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50
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Abstract
Functional elements in the genome express their function through physical association with particular proteins: transcription factors, components of the transcription machinery, specific histone modifications, and others. The genome-wide characterization of the protein-DNA interaction landscape of these proteins is thus a key approach toward the identification of candidate genomic regulatory regions. ChIP-seq (Chromatin Immunoprecipitation coupled with high-throughput sequencing) has emerged as the primary experimental methods for carrying out this task. Here, the ChIP-seq protocol is described together with some of the most important considerations for applying it in practice.
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