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Inferring Gene Regulatory Networks that control maintenance and identity of the Arabidopsis Root Stem Cells

ABSTRACT: We isolated QC cells and obtained their cell-type specific transcriptional profiles in a WT and in a pan mutant background by sorting GFP+ cells marked with pWOX5::GFP.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE97792 | GEO | 2017/09/18

SECONDARY ACCESSION(S): PRJNA382891

REPOSITORIES: GEO

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Inferring gene regulatory networks that control maintenance and identity of the Arabidopsis root stem cells

Project description:We isolated QC and xylem cells by sorting GFP+ cells marked with pWOX5::GFP and pTMO5::GFP respectively. We obtained cell-type specific transcriptional profiles of QC and xylem cells.

2017-09-18 | GSE76710 | GEO

From gene networks to network motif dynamics: how the presense of positive feed-back and -forward loops between PERIANTHIA, WUSCHEL-RELATED HOMEOBOX5 and GRF-INTERACTING FACTOR 1 modulates gene expression and function in the Arabidopsis roots.

Project description:We isolated QC and CEI cells and obtained their cell-type specific transcriptional profiles in a WT and in a wox5 mutant background by sorting GFP+ cells marked with pWOX5::GFP and pCYCD6::GFP.

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Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions [w5C6]

Project description:We performed a transcriptome analysis on FACS-sorted GFP positive cells from pCYCD6;1-GFP, wox5xpCYCD6;1-GFP, and pWOX5-GFP, and the GFP negative cells from pWOX5-GFP to obtain CEI specific transcriptional profiles in a WT and in a wox5 mutant background.

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Transcriptional profiling of the Arabidopsis root quiescent center

Project description:The Arabidopsis quiescent center (QC) is a small group of cells with low mitotic activity located at the center of the root stem cell niche. Its transcriptional profile was previously analyzed using two repeats of cells FACS isolated using the AGL42 marker. To get more power in analyzing QC transcriptional profile, we generated three additional samples of the QC, using the QC-specific marker WOX5. Three replicates of FACS-sorted GFP-positive cells from WOX5:GFP roots.

2014-12-17 | E-GEOD-64253 | biostudies-arrayexpress

Transcriptional profiling of the Arabidopsis root quiescent center

Project description:The Arabidopsis quiescent center (QC) is a small group of cells with low mitotic activity located at the center of the root stem cell niche. Its transcriptional profile was previously analyzed using two repeats of cells FACS isolated using the WOX5 marker. To get more power in analyzing QC transcriptional profile, we generated three additional samples of the QC, using the QC-specific marker WOX5.

2014-12-17 | GSE64253 | GEO

Vascular specific H3K27me3 and H3K4me3 profile in the Arabidopsis root

Project description:We isolated Vascular specific root protoplast using the pWOL:GFP marker line (Birnbaum et al., 2003) and Fluorescence Activated Cell Sorting (FACS). FACS-treated root protoplast from wild type plants (Col0) were used as control. The GFP positive protoplast from the pWOL:GFP line and WT protoplast were used for a ChIP-seq experiment using H3K27me3 and H3K4me3 antibodies.

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Project description:We directed expression of BLUEJAY, JACKDAW and SCARECROW through the UAS promoter in the J0571 line and performed cell sorting followed by microarray experiments to identify differentially expressed genes.

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Time course of the Arabidopsis root stem cells

Project description:The goal of this dataset was to transcriptionally profile the Arabidopsis root stem cells over developmental time. To accomplish this, we protoplasted roots expressing PET111:GFP every 8 hours from 4 days to 6 days old. We then collected GFP negative cells from the PET111:GFP line using cell sorting, as these cells represent the stem cell population. RNA was extracted from cells, libraries were prepared, and RNA-seq was performed. FPKM values were calulcated using Cufflinks.

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Identity of root peridermis cells undergoing suberization in Arabidopsis

Project description:In order to unravel the molecular processes involved in the nature of the root peridermis tissue, as well as in the suberin biosynthesis pathways occurring in this tissue, we have made use of Translating Ribosome Affinity Purification (TRAP) followed by RNA sequencing (TRAP-SEQ) on two marker lines; pUBQ10::BLRP-FLAG-GFP-RPL18 and pGPAT5::BLRP-FLAG-GFP-RPL18 line, after dissection of a zone of the root comprised between the root-hypocotyl junction and the first lateral root, allowing the respective selection of RNAs originating from all cells of the root segment, or only from those peridermis cells expressing the GPAT5 marker and therefore undergoing suberization.

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APC/CCCS52A2 repressed phytosulfokine signaling restricts root QC cell proliferation through ERF115 degradation

Project description:The quiescent center (QC) plays an essential role during root development by creating a microenvironment that preserves the stem cell fate of its surrounding cells. Strikingly, in order to retain root structure, QC cells only occasionally self-renew, displaying a proliferation rate far below that of all other cells within the root meristem. Previously, the APC/CCCS52A2 ubiquitine ligase and brassinosteroid signaling pathways have been found to antagonistically control Arabidopsis thaliana QC cell proliferation. Here, we demonstrate that both pathways converge on the ERF115 transcription factor that acts as a rate-limiting factor of QC cell division through transcriptional control of the autocrine phytosulfokine PSK5 peptide hormone. ERF115 marks QC cell division but is restrained through proteolysis by the APC/CCCS52A2 ubiquitine ligase, whereas QC proliferation is driven by brassinosteroid-dependent ERF115 expression. Combined, these two antagonistic mechanisms delimit the ERF115-PSK5 activity and QC renewal. Our results reveal a unique cell cycle regulatory mechanism that accounts for the low proliferation rate of QC cells within a surrounding population of highly mitotic active cells.

2013-11-04 | GSE48793 | GEO

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