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Khan T, Whyte JJ, Schulz LC, Roberts RM. Fluorescence-activated nuclear sorting (FANS) of nuclei from in vitro-generated syncytiotrophoblast. Placenta 2024:S0143-4004(24)00275-3. [PMID: 38944560 DOI: 10.1016/j.placenta.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
Large, multinucleated cells, like syncytiotrophoblasts (STB), are not readily analyzed by standard methods used for single cells, such as single-cell RNA-sequencing and fluorescence-activated cellular sorting (FACS). Here we have demonstrated that fluorescence-activated nuclear sorting (FANS) is suitable to analyze nuclei from STB. Human pluripotent stem cells (PSCs) can be differentiated into a mixed trophoblast populations comprising approximately 20 % STB by treatment with BMP4 (Bone Morphogenetic Protein-4), plus A83-01 and PD173074, inhibitors of activin and FGF2 signaling, respectively (the BAP model) in about a week. Here we demonstrate that FANS can be used to separate two types of STB nuclei from the nine different clusters of trophoblast nuclei previously identified in the BAP model by single nucleus RNA sequencing (snRNAseq). Rather than using cell surface markers, as in FACS, transcription factors in various combinations were employed to target specific nuclear types. Nuclei were isolated at d 8 of BAP differentiation of H1 human embryonic stem cells and fixed in 4 % paraformaldehyde. After permeabilization in 0.1 % triton X-100, nuclei were incubated for 3 and 1 h at 4 °C with primary and secondary antibodies respectively and nuclear samples were then subjected to FANS. By using markers identified by snRNA and immunohistochemistry, nuclei were first sorted into a Topoisomerase-1, or TOP1, bright population and then into the two STB subpopulations by using antibodies to JUNB (Jun B Proto-Oncogene) and TFCP2L1 (Transcription Factor CP2 Like 1). The protocol established here is simple, straightforward, and efficient and can be used on a relatively large scale to sort individual subtypes of nuclei from mixed populations of trophoblasts for further analysis.
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Affiliation(s)
- Teka Khan
- Department of Obstetrics, Gynecology, and Women's Health, School of Medicine, University of Missouri, Columbia, MO, United States; Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Jeffrey J Whyte
- Laboratory for Infectious Disease Research (LIDR), Division of Research, Innovation and Impact, University of Missouri, Columbia, MO, United States
| | - Laura C Schulz
- Department of Obstetrics, Gynecology, and Women's Health, School of Medicine, University of Missouri, Columbia, MO, United States
| | - R Michael Roberts
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States.
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Bradamante G, Nguyen VH, Incarbone M, Meir Z, Bente H, Donà M, Lettner N, Scheid OM, Gutzat R. Two ARGONAUTE proteins loaded with transposon-derived small RNAs are associated with the reproductive cell lineage in Arabidopsis. THE PLANT CELL 2024; 36:863-880. [PMID: 38060984 PMCID: PMC10980394 DOI: 10.1093/plcell/koad295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 11/23/2023] [Indexed: 04/01/2024]
Abstract
In sexually propagating organisms, genetic, and epigenetic mutations are evolutionarily relevant only if they occur in the germline and are hence transmitted to the next generation. In contrast to most animals, plants are considered to lack an early segregating germline, implying that somatic cells can contribute genetic information to progeny. Here we demonstrate that 2 ARGONAUTE proteins, AGO5 and AGO9, mark cells associated with sexual reproduction in Arabidopsis (Arabidopsis thaliana) throughout development. Both AGOs are loaded with dynamically changing small RNA populations derived from highly methylated, pericentromeric, long transposons. Sequencing of single stem cell nuclei revealed that many of these transposons are co-expressed within an AGO5/9 expression domain in the shoot apical meristem (SAM). Co-occurrence of transposon expression and specific ARGONAUTE (AGO) expression in the SAM is reminiscent of germline features in animals and supports the existence of an early segregating germline in plants. Our results open the path to investigating transposon biology and epigenome dynamics at cellular resolution in the SAM stem cell niche.
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Affiliation(s)
- Gabriele Bradamante
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Vu Hoang Nguyen
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Marco Incarbone
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Zohar Meir
- Faculty of Mathematics and Computer Science & Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Heinrich Bente
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Mattia Donà
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Nicole Lettner
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Ruben Gutzat
- Austrian Academy of Sciences, Vienna Biocenter (VBC), Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
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Berendzen KW, Grefen C, Sakamoto T, Slane D. Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry. Methods Mol Biol 2023; 2698:57-73. [PMID: 37682469 DOI: 10.1007/978-1-0716-3354-0_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: 09/09/2023]
Abstract
The past two decades in biomedical research have experienced an explosion of cell type-specific and single-cell studies, especially concerning the concomitant dissection of regulatory and transcriptional landscapes of those under investigation. Additionally, leveraging next-generation sequencing (NGS) platforms efforts have been undertaken to evaluate the effects of chromatin accessibility, histone modifications, or even transcription factor binding sites. We have shown that Fluorescence-Activated Nuclear Sorting (FANS) is an effective means to characterize the transcriptomes of nuclei from different tissues. In light of our own technical and experimental developments, we extend this effort to combine FACS/FANS with Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) for profiling individual cell types according to their chromatin and transcriptional states.
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Affiliation(s)
- Kenneth W Berendzen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Christopher Grefen
- Faculty of Biology and Biotechnology, Molecular and Cellular Botany, University of Bochum, Bochum, Germany
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Daniel Slane
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan.
- The University of Tokyo, Graduate School of Frontier Sciences, Department of Integrated Biosciences, Laboratory of Integrated Biology, Chiba, Japan.
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Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis. Sci Rep 2022; 12:111. [PMID: 34997061 PMCID: PMC8741915 DOI: 10.1038/s41598-021-04056-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
Opium poppy (Papaver somniferum) is one of the world’s oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop.
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Moro B, Kisielow M, Borrero VB, Bouet A, Brosnan CA, Bologna NG. Nuclear RNA purification by flow cytometry to study nuclear processes in plants. STAR Protoc 2021; 2:100320. [PMID: 33659901 PMCID: PMC7890302 DOI: 10.1016/j.xpro.2021.100320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nature of plant tissues has continuously hampered understanding of the spatio-temporal and subcellular distribution of RNA-guided processes. Here, we describe a universal protocol based on Arabidopsis to investigate subcellular RNA distribution from virtually any plant species using flow cytometry sorting. This protocol includes all necessary control steps to assess the quality of the nuclear RNA purification. Moreover, it can be easily applied to different plant developmental stages, tissues, cell cycle phases, experimental growth conditions, and specific cell type(s). For complete information on the use and execution of this protocol, please refer to Bologna et al. (2018) and de Leone et al. (2020). Isolation of highly pure nuclear RNA from essentially any plant species Full procedure describing key steps for quality validation of nuclear RNA purification Applicable to different tissues, cell cycle phases, stresses, or specific cell types
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Affiliation(s)
- Belén Moro
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | | | | | - Antoine Bouet
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Christopher A Brosnan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nicolás G Bologna
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
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Gutzat R, Rembart K, Nussbaumer T, Hofmann F, Pisupati R, Bradamante G, Daubel N, Gaidora A, Lettner N, Donà M, Nordborg M, Nodine M, Mittelsten Scheid O. Arabidopsis shoot stem cells display dynamic transcription and DNA methylation patterns. EMBO J 2020; 39:e103667. [PMID: 32815560 PMCID: PMC7560203 DOI: 10.15252/embj.2019103667] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022] Open
Abstract
In plants, aerial organs originate continuously from stem cells in the center of the shoot apical meristem. Descendants of stem cells in the subepidermal layer are progenitors of germ cells, giving rise to male and female gametes. In these cells, mutations, including insertions of transposable elements or viruses, must be avoided to preserve genome integrity across generations. To investigate the molecular characteristics of stem cells in Arabidopsis, we isolated their nuclei and analyzed stage‐specific gene expression and DNA methylation in plants of different ages. Stem cell expression signatures are largely defined by developmental stage but include a core set of stem cell‐specific genes, among which are genes implicated in epigenetic silencing. Transiently increased expression of transposable elements in meristems prior to flower induction correlates with increasing CHG methylation during development and decreased CHH methylation, before stem cells enter the reproductive lineage. These results suggest that epigenetic reprogramming may occur at an early stage in this lineage and could contribute to genome protection in stem cells during germline development.
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Affiliation(s)
- Ruben Gutzat
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Klaus Rembart
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas Nussbaumer
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Falko Hofmann
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Rahul Pisupati
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Gabriele Bradamante
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Nina Daubel
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Angelika Gaidora
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Nicole Lettner
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Mattia Donà
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Michael Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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