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A gene expression map of Arabidopsis thaliana shoot apical meristem stem cell niche

ABSTRACT: A gene expression map of Arabidopsis thaliana shoot apical meristem stem cell niche was generated by isolating the specific cell type using the cell sorting methods. We used ap1-1;cal1-1 mutant background to enrich the sufficient number of cells for microarray analysis. Spatial and temporal regulation of gene expression is critical for stem-cell homeostasis. The shoot apical meristems of Arabidopsis thaliana harbor a small set of stem-cells which are surrounded by several million differentiating cells, imposing a severe limitation on the genomic analyses of stem-cell homeostasis. We have employed cell type-specific gene expression profiling that allowed us to generate a high-resolution gene expression map and it has revealed gene expression networks specific to the cell types of the stem-cell niche. We demonstrate that the expression map can be used to predict in vivo gene expression domains to identify novel gene expression patterns. Furthermore, it has revealed molecular pathways that are conserved among plant and animal stem-cell populations. The expression map should guide future reverse genetics experiments, high-resolution analyses of cell-cell communication networks and epigenetic modifications. Keywords: cell type comparison

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE13596 | GEO | 2009/04/06

SECONDARY ACCESSION(S): PRJNA110659

REPOSITORIES: GEO

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Transcription profiling of Arabidopsis thaliana shoot apical meristem stem cell niche

Project description:A gene expression map of Arabidopsis thaliana shoot apical meristem stem cell niche was generated by isolating the specific cell type using the cell sorting methods. We used ap1-1;cal1-1 mutant background to enrich the sufficient number of cells for microarray analysis. Spatial and temporal regulation of gene expression is critical for stem-cell homeostasis. The shoot apical meristems of Arabidopsis thaliana harbor a small set of stem-cells which are surrounded by several million differentiating cells, imposing a severe limitation on the genomic analyses of stem-cell homeostasis. We have employed cell type-specific gene expression profiling that allowed us to generate a high-resolution gene expression map and it has revealed gene expression networks specific to the cell types of the stem-cell niche. We demonstrate that the expression map can be used to predict in vivo gene expression domains to identify novel gene expression patterns. Furthermore, it has revealed molecular pathways that are conserved among plant and animal stem-cell populations. The expression map should guide future reverse genetics experiments, high-resolution analyses of cell-cell communication networks and epigenetic modifications. Experiment Overall Design: Three replicates were used CLV3p, CLV3n and FILp, while for WUSp only two replicates were used. CLV3n cells lacks CLV3p cell type.

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Arabidopsis thaliana

Project description:A gene expression map of Arabidopsis thaliana shoot apical meristem stem cell niche

| PRJNA110659 | ENA

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Project description:Zygote division and stem cell homeostasis are crucial events for plant development. Here, we found that mutations in DEAD-box RNA helicase 27 (RH27) affected zygote division and stem cell homeostasis in Arabidopsis (Arabidopsis thaliana). The strong mutant allele rh27-1 showed a zygote-lethal phenotype, while the weak mutant allele rh27-2 showed defective embryogenesis and compromised stem cell homeostasis in both the shoot apical meristem (SAM) and root apical meristem (RAM). RH27 was expressed in embryos from the zygote stage, and in the SAM and RAM. Cytological analyses revealed that stem cell homeostasis in the SAM and RAM was disrupted in rh27-2. Then, the expression levels of genes related to stem cell homeostasis were elevated in rh27-2, which coincides with down-regulations of their corresponding negative regulatory microRNAs. Furthermore, small RNA-sequencing indicated that the reduction of miRNAs was a global effect in both shoot apices and root tips of rh27-2. Additionally, the accumulation of pri-miRNAs was detected to be decreased. Biochemical studies showed that the nucleus-localized RH27 interacted directly with SERRATE, a component of the microprocessor complex, and DAWDLE, which facilitates the recruitment of substrates to the complex, suggesting that RH27 is a subunit of the microprocessor complex. Overall, this work provides evidences that RH27 regulates zygote division and stem cell homeostasis in Arabidopsis through miRNA biogenesis.

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