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Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting

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Plant Gene Regulatory Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1629))

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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References

  1. Mayer U, Jürgens G (1998) Pattern formation in plant embryogenesis: a reassessment. Semin Cell Dev Biol 9:187–193. doi:10.1006/scdb.1997.0210

    Article  CAS  PubMed  Google Scholar 

  2. Galbraith DW, Birnbaum K (2006) Global studies of cell type-specific gene expression in plants. Annu Rev Plant Biol 57:451–475. doi:10.1146/annurev.arplant.57.032905.105302

    Article  CAS  PubMed  Google Scholar 

  3. Gautam V, Sarkar AK (2015) Laser assisted microdissection, an efficient technique to understand tissue specific gene expression patterns and functional genomics in plants. Mol Biotechnol 57:299–308. doi:10.1007/s12033-014-9824-3

    Article  CAS  PubMed  Google Scholar 

  4. Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, Galbraith DW et al (2005) Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nat Methods 2:615–619. doi:10.1038/nmeth0805-615

    Article  CAS  PubMed  Google Scholar 

  5. Iyer-Pascuzzi AS, Benfey PN (2010) Fluorescence-activated cell sorting in plant developmental biology. Methods Mol Biol 655:313–319. doi:10.1007/978-1-60761-765-5_21

    Article  CAS  PubMed  Google Scholar 

  6. Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW et al (2003) A gene expression map of the Arabidopsis root. Science 302:1956–1960. doi:10.1126/science.1090022

    Article  CAS  PubMed  Google Scholar 

  7. Brady SM, Orlando DA, Lee J-Y, Wang JY, Koch J, Dinneny JR et al (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318:801–806. doi:10.1126/science.1146265

    Article  CAS  PubMed  Google Scholar 

  8. Deal RB, Henikoff S (2011) The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat Protoc 6:56–68. doi:10.1038/nprot.2010.175

    Article  CAS  PubMed  Google Scholar 

  9. Zhang C, Barthelson RA, Lambert GM, Galbraith DW (2008) Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiol 147:30–40. doi:10.1104/pp.107.115246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Slane D, Kong J, Schmid M, Jürgens G, Bayer M (2015) Profiling of embryonic nuclear vs. cellular RNA in Arabidopsis thaliana. Genom Data 4:96–98. doi:10.1016/j.gdata.2015.03.015

    Article  PubMed  PubMed Central  Google Scholar 

  11. Slane D, Kong J, Berendzen KW, Kilian J, Henschen A, Kolb M et al (2014) Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development 141:4831–4840. doi:10.1242/dev.116459

    Article  CAS  PubMed  Google Scholar 

  12. Khodosevich K, Inta D, Seeburg PH, Monyer H (2007) Gene expression analysis of in vivo fluorescent cells. PLoS One 2. doi:10.1371/journal.pone.0001151

  13. Weinhofer I, Köhler C (2014) Plant epigenetics and epigenomics. Methods Mol Biol 1112:105–115. doi:10.1007/978-1-62703-773-0

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The research in our group is funded by the DFG (Deutsche Forschungsgemeinschaft, BA3356/2-1 and SFB1101 to M.B.) and the Max Planck Society. This protocol is based on previously published work [11]. We like to thank Joachim Kilian, Kenneth W. Berendzen, Jixiang Kong, and Gerd Jürgens for the support and help in establishing the initial protocol.

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Authors and Affiliations

  1. Department of Cell Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tuebingen, Germany

    Daniel Slane & Martin Bayer

Authors
  1. Daniel Slane
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  2. Martin Bayer
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Corresponding author

Correspondence to Martin Bayer .

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Editors and Affiliations

  1. Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany

    Kerstin Kaufmann

  2. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Bernd Mueller-Roeber

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Slane, D., Bayer, M. (2017). Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting. In: Kaufmann, K., Mueller-Roeber, B. (eds) Plant Gene Regulatory Networks. Methods in Molecular Biology, vol 1629. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7125-1_3

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  • DOI: https://doi.org/10.1007/978-1-4939-7125-1_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7124-4

  • Online ISBN: 978-1-4939-7125-1

  • eBook Packages: Springer Protocols

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