1
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You Y, Jiang Z. The eINTACT method for studying nuclear changes in host plant cells targeted by bacterial effectors in native infection contexts. Nat Protoc 2023; 18:3173-3193. [PMID: 37697105 DOI: 10.1038/s41596-023-00879-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/23/2023] [Indexed: 09/13/2023]
Abstract
Type-III effector proteins are major virulence determinants that most gram-negative bacteria inject into host cells to manipulate cellular processes for infection. Because effector-targeted cells are embedded and underrepresented in infected plant tissues, it is technically challenging to isolate them for focused studies of effector-induced cellular changes. This protocol describes a novel technique, effector-inducible isolation of nuclei tagged in specific cell types (eINTACT), for isolating biotin-labeled nuclei from Arabidopsis plant cells that have received Xanthomonas bacterial effectors by using streptavidin-coated magnetic beads. This protocol is an extension of the existing Nature Protocols Protocol of the INTACT method for the affinity-based purification of nuclei of specific cell types in the context of developmental biology. In a phytopathology scenario, our protocol addresses how to obtain eINTACT transgenic lines and compatible bacterial mutants, verify the eINTACT system and purify nuclei of bacterial effector-recipient cells from infected tissues. Differential analyses of purified nuclei from plants infected by bacteria expressing the effector of interest and those from plants infected by effector-deletion bacterial mutants will reveal the effector-dependent nuclear changes in targeted host cells. Provided that the eINTACT system is available, the infection experiment takes 5 d, and the procedures, from collecting bacteria-infected leaves to obtaining nuclei of effector-targeted cells, can be completed in 4 h. eINTACT is a unique method for isolating high-quality nuclei from bacterial effector-targeted host cells in native infection contexts. This method is adaptable to study the functions of type-III effectors from numerous gram-negative bacteria in host plants that are amenable to transformation.
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Affiliation(s)
- Yuan You
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany.
- Department of General Genetics, Center for Plant Molecular Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany.
| | - Zhihao Jiang
- Department of Plant Biochemistry, Center for Plant Molecular Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany
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2
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Abstract
High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells. We particularly highlight their impact on plant cell identity, including unprecedented views of cell transitions and definitions of rare and novel cell types. We also point out current challenges and future opportunities for the application and analyses of single-cell transcriptomics in plants. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - Yan Zhu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; , ,
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3
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Picard CL, Povilus RA, Williams BP, Gehring M. Transcriptional and imprinting complexity in Arabidopsis seeds at single-nucleus resolution. NATURE PLANTS 2021; 7:730-738. [PMID: 34059805 PMCID: PMC8217372 DOI: 10.1038/s41477-021-00922-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/15/2021] [Indexed: 05/06/2023]
Abstract
Seeds are a key life cycle stage for many plants. Seeds are also the basis of agriculture and the primary source of calories consumed by humans1. Here, we employ single-nucleus RNA-sequencing to generate a transcriptional atlas of developing Arabidopsis thaliana seeds, with a focus on endosperm. Endosperm, the primary site of gene imprinting in flowering plants, mediates the relationship between the maternal parent and the embryo2. We identify transcriptionally uncharacterized nuclei types in the chalazal endosperm, which interfaces with maternal tissue for nutrient unloading3,4. We demonstrate that the extent of parental bias of maternally expressed imprinted genes varies with cell-cycle phase, and that imprinting of paternally expressed imprinted genes is strongest in chalazal endosperm. Thus, imprinting is spatially and temporally heterogeneous. Increased paternal expression in the chalazal region suggests that parental conflict, which is proposed to drive imprinting evolution, is fiercest at the boundary between filial and maternal tissues.
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Affiliation(s)
- Colette L Picard
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Ben P Williams
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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4
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Slane D, Berendzen KW, Witthöft J, Jürgens G. Transcriptomic Profiling of the Arabidopsis Embryonic Epidermis Using FANS in Combination with RNAseq. Methods Mol Biol 2021; 2122:151-164. [PMID: 31975302 DOI: 10.1007/978-1-0716-0342-0_12] [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: 03/01/2023]
Abstract
The fundamental mechanisms of cell identity and tissue establishment are important already from the very beginning of a plant's life and reiterate later during development. In order to unravel and understand the underlying mechanisms to generate differences that in turn lead to cell or tissue types, plant cells have to be separated and their transcriptional setup analyzed. We have previously demonstrated that fluorescence-activated nuclear sorting (FANS) is a powerful tool to generate nuclear transcriptomic profiles of the most inaccessible embryonic tissues. In this protocol, we extend this effort to combine FANS with next generation RNA sequencing (RNA-seq) to achieve early embryonic transcriptomes of Arabidopsis epidermis precursor tissue (protoderm) and the inner tissue counterpart.
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Affiliation(s)
- Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kenneth W Berendzen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Janika Witthöft
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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5
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Borg M, Papareddy RK, Dombey R, Axelsson E, Nodine MD, Twell D, Berger F. Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis. eLife 2021; 10:e61894. [PMID: 33491647 PMCID: PMC7920552 DOI: 10.7554/elife.61894] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements. This event is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilisation. Hence, distinct epigenetic reprogramming events rewire transcription through major reorganisation of the regulatory epigenome to guide the alternation of generations in flowering plants.
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Affiliation(s)
- Michael Borg
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | | | - Rodolphe Dombey
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - Elin Axelsson
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - Michael D Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
| | - David Twell
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
- Department of Genetics, University of LeicesterLeicesterUnited Kingdom
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of SciencesViennaAustria
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6
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Van den Broeck L, Gordon M, Inzé D, Williams C, Sozzani R. Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling. Front Genet 2020; 11:457. [PMID: 32547596 PMCID: PMC7270862 DOI: 10.3389/fgene.2020.00457] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/14/2020] [Indexed: 12/26/2022] Open
Abstract
Plant responses to environmental and intrinsic signals are tightly controlled by multiple transcription factors (TFs). These TFs and their regulatory connections form gene regulatory networks (GRNs), which provide a blueprint of the transcriptional regulations underlying plant development and environmental responses. This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs. Additionally, this review describes network inference techniques that leverage gene expression data to predict regulatory interactions. These computational and experimental methodologies yield complex networks that can identify new regulatory interactions, driving novel hypotheses. Biological properties that contribute to the complexity of GRNs are also described in this review. These include network topology, network size, transient binding of TFs to DNA, and competition between multiple upstream regulators. Finally, this review highlights the potential of machine learning approaches to leverage gene expression data to predict phenotypic outputs.
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Affiliation(s)
- Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Max Gordon
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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7
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Abstract
Transcriptomic studies have proven powerful and effective as a tool to study the molecular underpinnings of plant development. Still, it remains challenging to disentangle cell- or tissue-specific transcriptomes in complex structures like the plant seed. In particular, the embryo of flowering plants is embedded in the endosperm, a nurturing tissue, which, in turn, is enclosed by the maternal seed coat. Here, we describe laser-assisted microdissection (LAM) to isolate highly pure embryo tissue from whole seeds. This technique is applicable to virtually any plant seed, and we illustrate the use of LAM to isolate embryos from species of the Boechera and Solanum genera. LAM is a tool that will greatly help to increase the repertoires of tissue-specific transcriptomes, including those of embryos and parts thereof, in nonmodel plants.
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8
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Kubo M, Nishiyama T, Tamada Y, Sano R, Ishikawa M, Murata T, Imai A, Lang D, Demura T, Reski R, Hasebe M. Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation. Nucleic Acids Res 2019; 47:4539-4553. [PMID: 30873540 PMCID: PMC6511839 DOI: 10.1093/nar/gkz181] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 03/01/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
Next-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression that cannot be studied using populations of cells. The utilization of scRNA-seq is, however, restricted to cell types that can be isolated from their original tissues, and it can be difficult to obtain precise positional information for these cells in situ. Here, we established single cell-digital gene expression (1cell-DGE), a method of scRNA-seq that uses micromanipulation to extract the contents of individual living cells in intact tissue while recording their positional information. With 1cell-DGE, we could detect differentially expressed genes (DEGs) during the reprogramming of leaf cells of the moss Physcomitrella patens, identifying 6382 DEGs between cells at 0 and 24 h after excision. Furthermore, we identified a subpopulation of reprogramming cells based on their pseudotimes, which were calculated using transcriptome profiles at 24 h. 1cell-DGE with microcapillary manipulation can be used to analyze the gene expression of individual cells without detaching them from their tightly associated tissues, enabling us to retain positional information and investigate cell-cell interactions.
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Affiliation(s)
- Minoru Kubo
- Institute for Research Initiative, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan
| | - Yosuke Tamada
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Masaki Ishikawa
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Takashi Murata
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
| | - Akihiro Imai
- Faculty of Life Sciences, Hiroshima Institute of Technology, Hiroshima 731-5193, Japan
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,Signaling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,School of Life Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
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9
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Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons. Sci Rep 2019; 9:8350. [PMID: 31171808 PMCID: PMC6554355 DOI: 10.1038/s41598-019-44798-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 05/24/2019] [Indexed: 12/25/2022] Open
Abstract
Subcellular RNAseq promises to dissect transcriptional dynamics but is not well characterized. Furthermore, FACS may introduce bias but has not been benchmarked genome-wide. Finally, D1 and D2 dopamine receptor-expressing medium spiny neurons (MSNs) of the nucleus accumbens (NAc) are fundamental to neuropsychiatric traits but have only a short list of canonical surface markers. We address these gaps by systematically comparing nuclear-FACS, whole cell-FACS, and RiboTag affinity purification from D1- and D2-MSNs. Using differential expression, variance partitioning, and co-expression, we identify the following trade-offs for each method. RiboTag-seq best distinguishes D1- and D2-MSNs but has the lowest transcriptome coverage. Nuclear-FACS-seq generates the most differentially expressed genes and overlaps significantly with neuropsychiatric genetic risk loci, but un-annotated genes hamper interpretation. Whole cell-FACS is more similar to nuclear-FACS than RiboTag, but captures aspects of both. Using pan-method approaches, we discover that transcriptional regulation is predominant in D1-MSNs, while D2-MSNs tend towards cytosolic regulation. We are also the first to find evidence for moderate sexual dimorphism in these cell types at baseline. As these results are from 49 mice (nmale = 39, nfemale = 10), they represent generalizable ground-truths. Together, these results guide RNAseq methods selection, define MSN transcriptomes, highlight neuronal sex differences, and provide a baseline for D1- and D2-MSNs.
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10
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Palovaara J, Weijers D. Adapting INTACT to analyse cell-type-specific transcriptomes and nucleocytoplasmic mRNA dynamics in the Arabidopsis embryo. PLANT REPRODUCTION 2019; 32:113-121. [PMID: 30430248 DOI: 10.1007/s00497-018-0347-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/31/2018] [Indexed: 05/06/2023]
Abstract
In the early embryo of vascular plants, the different cell types and stem cells of the seedling are specified as the embryo develops from a zygote towards maturity. How the key steps in cell and tissue specification are instructed by genome-wide transcriptional activity is poorly understood. Progress in defining transcriptional regulation at the genome-wide level in plant embryos has been hampered by difficulties associated with capturing cell-type-specific transcriptomes in this small and inaccessible structure. We recently adapted a two-component genetic nucleus labelling system called INTACT to isolate nuclei from distinct cell types at different stages of Arabidopsis thaliana embryogenesis. We have used these to generate a transcriptomic atlas of embryo development following microarray-based expression profiling. Here, we present a general description of the adapted INTACT procedure, including the two-component labelling system, seed isolation, nuclei preparation and purification, as well as transcriptomic profiling. We also compare nuclear and cellular transcriptomes from the early Arabidopsis embryo to assess nucleocytoplasmic differences and discuss how these differences can be used to infer regulation of gene activity.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Molecular Genetics, University of Bremen, 28359, Bremen, Germany
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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11
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Abstract
Fluorescence-activated cell sorting (FACS) is a powerful method for the analysis of cell type-specific transcriptome profiles, DNA or histone modifications, and chemical compounds. In plants, it has been employed mainly with root and shoot tissue in combination with cell wall digestion on cellular and nuclear content. However, many tissues are recalcitrant to cell separation and are therefore not readily accessible for FACS analysis. Here, we lay out a detailed protocol for the generation of transcriptional profiles from fluorescently labeled nuclei. The protocol described in this chapter has been used successfully to generate a transcriptional map of the early Arabidopsis thaliana embryo.
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12
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Abstract
Plants, like other eukaryotes, have evolved complex mechanisms to coordinate gene expression during development, environmental response, and cellular homeostasis. Transcription factors (TFs), accompanied by basic cofactors and posttranscriptional regulators, are key players in gene-regulatory networks (GRNs). The coordinated control of gene activity is achieved by the interplay of these factors and by physical interactions between TFs and DNA. Here, we will briefly outline recent technological progress made to elucidate GRNs in plants. We will focus on techniques that allow us to characterize physical interactions in GRNs in plants and to analyze their regulatory consequences. Targeted manipulation allows us to test the relevance of specific gene-regulatory interactions. The combination of genome-wide experimental approaches with mathematical modeling allows us to get deeper insights into key-regulatory interactions and combinatorial control of important processes in plants.
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Affiliation(s)
- Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Dijun Chen
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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13
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Chitikova Z, Steiner FA. Cell type-specific epigenome profiling using affinity-purified nuclei. Genesis 2016; 54:160-9. [PMID: 26789661 DOI: 10.1002/dvg.22919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 11/08/2022]
Abstract
The development of a multicellular organism from a single zygote depends on the differentiation of progenitor cells to specialized cell types. The differentiation of these cell types is associated with changes in gene expression and the underlying chromatin landscape. To understand how these processes are regulated, it is desirable to understand how the chromatin features that constitute the epigenome differ between cell types at any given time during development. INTACT, a method for the cell type-specific purification of nuclei that can be used for the isolation of both RNA and chromatin, has emerged as a powerful tool to simultaneously study gene expression and chromatin profiles specifically in cell types of interest. In this review, we focus on the application of INTACT to different model organisms and discuss its potential for profiling cell types in their developmental context.
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Affiliation(s)
- Zhanna Chitikova
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology, Sciences III, University of Geneva, Geneva, Switzerland
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