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Cell type specific gene expression map of Arabidopsis thaliana SAM.

ABSTRACT: Shoot apical meristem (SAM) of higher plant composed of a few distinct cell types. All the cells in a mature plant’s SAM derived from 30~35 stem cells reservoir which are located at the tip of the apex. Plants ability to give rise diverse cell types from a pool of pluripotent stem cells requires orchestrated gene network that controls the cell fate commitment during the meristem development. To understand, how gene regulatory networks control cell identities switches during cell differentiation requires resolution in recording their gene expression pattern at single cell resolution. An earlier expression map involving three-cell population of stem cell niche revealed complex expression pattern among the cell types1. We developed this approach further and report here a gene expression map using cell-sorting methods for fluorescent protein marked cells in Arabidopsis shoot. The map covered 10 cell populations. This gene expression map represents data from 10 different cell types from Arabidopsis SAM. It will be first step in defining the function of many unknown genes in model plant Arabidopsis.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE28109 | GEO | 2014/05/15

SECONDARY ACCESSION(S): PRJNA139823

REPOSITORIES: GEO

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Cell type specific gene expression map of Arabidopsis thaliana SAM.

Project description:Shoot apical meristem (SAM) of higher plant composed of a few distinct cell types. All the cells in a mature plant’s SAM derived from 30~35 stem cells reservoir which are located at the tip of the apex. Plants ability to give rise diverse cell types from a pool of pluripotent stem cells requires orchestrated gene network that controls the cell fate commitment during the meristem development. To understand, how gene regulatory networks control cell identities switches during cell differentiation requires resolution in recording their gene expression pattern at single cell resolution. An earlier expression map involving three-cell population of stem cell niche revealed complex expression pattern among the cell types1. We developed this approach further and report here a gene expression map using cell-sorting methods for fluorescent protein marked cells in Arabidopsis shoot. The map covered 10 cell populations. This gene expression map represents data from 10 different cell types from Arabidopsis SAM. It will be first step in defining the function of many unknown genes in model plant Arabidopsis. Based on the in situ hybridization we identified 7 new cell types specific gene expression patterns. The promoters of these genes were used to generate fluorescent reporters. After treating the SAM with protoplasting cocktail, we sorted the fluorescent protein tagged cells using fluorescent activated cell sorter (FACS). The purified cell population was used to isolate RNA. Two round of RNA amplification was performed before microarray hybridization.

2014-05-15 | E-GEOD-28109 | biostudies-arrayexpress

Transcriptomic analysis of REVOLUTA and mir165a cell-types of Arabidopsis shoot apical meristem

Project description:Dorso-ventral (DV) patterning at the Shoot Apical meristem (SAM) is essential for organogenesis in Arabidopsis. Dorsal and ventral gene expressed domains are separated by boundaries from where the new organ initiation starts. Here by using cell-types specific transcriptomics approach, we have identified dorsal, ventral and boundary specific genes in SAM.

2023-12-20 | GSE221138 | GEO

Transcriptomic analysis of dorso-ventral cell-types of Arabidopsis shoot apical meristem

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Proteome of rice shoot apical meristem

Project description:DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we found that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also found that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs.

2020-08-14 | PXD020608 | Pride

A gene expression map 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. Keywords: cell type comparison

2009-04-06 | GSE13596 | GEO

Genetic networks regulating structure and function of the maize shoot apical meristem

Project description:The shoot apical meristem (SAM) of plants, a specialized stem cell niche at the growing shoot tip, integrates developmental and environmental signals to direct the initiation and patterning of new organs such as leaves. Its activity throughout the plant's lifetime is tightly controlled. To gain insight into gene regulatory networks behind stem cell maintenance and organogenesis, we generated a high-resolution gene expression atlas of distinct domains and cell types within the vegetative shoot apex of 14 day-old maize B73 seedlings using laser microdissection and RNA deep sequencing. Data for 9 domains was previously released under SRA: SRP101301. This release adds data for biological duplicate samples collected for the SAM central zone, and the adaxial and abaxial sides of leaf primordia.

2019-10-02 | GSE137715 | GEO

Transcription profiling of Arabidopsis thaliana shoot apical meristem stem cell niche

2009-04-11 | E-GEOD-13596 | biostudies-arrayexpress

DEAD-box RNA helicase 27-Mediated MicroRNA Biogenesis Is Essential for Zygote Division and Stem Cell Homeostasis in Arabidopsis

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.

2021-05-26 | GSE154473 | GEO

Genome-wide analysis of gene expression in the soybean shoot apical meristem

Project description:The shoot apical meristem (SAM) contains undifferentiated stem cells that are responsible for the initiation of above-ground organs, and eventually the general architecture of the plant. To gain insight into the nature of genetic programs and the regulatory networks underlying SAM function in soybean, we have used Affymetrix soybean GeneChip® to investigate the transcript profiles associated with micro-dissected SAMs or axillary meristems (AMs). While the microarray data disclosed the conservation of transcriptional signature between the two types of meristems, subsequent comparison of SAM transcript profile with that of non-meristem (NM) tissue revealed a total of 1090 and 1523 transcripts that are significantly up- or down-regulated in the SAM. Further in situ hybridization analysis on selected transcripts has implicated their roles in SAM maintenance and the establishment of organ polarity. We also identified a gene that could potentially serve as a novel marker that distinguishes the differentiating cells in the meristem from the pluripotent stem cells. Along with many unknowns, transcripts with putative annotation have also been identified that has allowed us to infer SAM regulatory roles for various families of transcription factors as well as products associated with auxin-mediated responses, cell division and proliferation, epigenetic regulation, miRNA regulation and protein turnover. Computational analysis on the promoter regions of Arabidopsis orthologs of genes with high expression in the soybean SAM revealed a conserved over-representation of three cis-acting regulatory motifs. Our microarray data thus represents a rich source of target genes for further study into the meristem function and maintenance. Keywords: meristem transcript profile

2009-02-20 | GSE10607 | GEO

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Project description:Due to the major limitation of small set of stem cells located in the Shoot Apical Meristem (SAM), it is difficult to perform the whole genome analysis specific for those stem cells. Here, we generated the mp clv3 double mutant with a larger Shoot Apical Meristem,in which shoot stem cells were drastically enriched while the differentiation of stem cells was blocked. Then we performed the mRNA profiling on wild type and mp clv3 double mutant. And this could offer an ideal genetic material to highly increase the resolution of plant shoot stem cell profiling, also to further explore the mechanism of plant stem-cell regulation.

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