title: Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo.
abstract: In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.
authors.affiliation: Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Slane
authors.affiliation: Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany.
authors.forename: Jixiang
authors.initials: J
authors.lastname: Kong
authors.affiliation: Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany.
authors.forename: Kenneth W
authors.initials: KW
authors.lastname: Berendzen
authors.affiliation: Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany.
authors.forename: Joachim
authors.initials: J
authors.lastname: Kilian
authors.affiliation: Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
authors.forename: Agnes
authors.initials: A
authors.lastname: Henschen
authors.affiliation: Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
authors.forename: Martina
authors.initials: M
authors.lastname: Kolb
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Schmid
authors.affiliation: Department of Plant Physiology, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany.
authors.forename: Klaus
authors.initials: K
authors.lastname: Harter
authors.affiliation: Microscopy facility, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Mayer
authors.affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent B-9052, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent B-9052, Belgium Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK.
authors.forename: Ive
authors.initials: I
authors.lastname: De Smet
authors.affiliation: Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Bayer
authors.affiliation: Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen 72076, Germany gerd.juergens@zmbp.uni-tuebingen.de.
authors.forename: Gerd
authors.initials: G
authors.lastname: Jürgens
mesh_terms: D017360:Arabidopsis / Q000196:embryology* / Q000378:metabolism; D002467:Cell Nucleus / Q000737:chemistry*; D003001:Cloning, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D005838:Genotype; D017403:In Situ Hybridization; D046228:Microarray Analysis; D008856:Microscopy, Fluorescence; D015138:RNA, Nuclear / Q000302:isolation & purification*; D060888:Real-Time Polymerase Chain Reaction; D012639:Seeds / Q000378:metabolism*
chemical_list: D015138:RNA, Nuclear
keywords: Fluorescence-activated nuclear sorting; Proembryo; Suspensor; Transcriptome analysis