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Transcriptional profiling of the Arabidopsis root quiescent center

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE64253 | GEO | 2014/12/17

SECONDARY ACCESSION(S): PRJNA270538

REPOSITORIES: GEO

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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

Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots

Project description:Understanding stem cell regulatory circuits is the next challenge in plant biology, as these cells are essential for tissue growth and organ regeneration in response to stress. In the Arabidopsis primary root apex, stem-cell specific transcription factors BRAVO and WOX5 co-localize in the Quiescent Center (QC) cells, where they commonly repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Genetic and biochemical analysis indicates that BRAVO and WOX5 form a transcription factor complex that modulates gene expression in the QC cells to preserve overall root growth and architecture. Furthermore, by using mathematical modeling we establish that BRAVO uses the WOX5/BRAVO complex to promote WOX5 activity in the stem cells. Our results unveil the importance of transcriptional regulatory circuits in plant stem cell development.

2021-05-06 | GSE173945 | GEO

Single-cell RNA-seq for pGL2 and QC cells from the Arabidopsis thaliana root

Project description:To demonstrate our method of controlling for technical noise in single-cell RNA-seq experiments we manually collected single A. thaliana cells marked by the expression of green fluorescent protein (GFP) driven by either the GL2 or WOX5 promoters. Seven and six cells were collected from each cell type, respectively. The GL2 promoter marks the non-hair cells in the root epidermis whereas the WOX5 promoter specifies the quiescent center (QC) of the root. Each cell selected was processed together with 50 pg of total HeLa RNA spike-in to prepare RNA-seq libraries using the Tang protocol. For comparison, we again added the commercially available ERCC spike-ins. We also performed RNA-seq on a set of technical replicates of total A. thaliana RNA using starting amounts ranging from 5000pg down to 10pg, a range that covers the RNA content obtainable from single cells of various sizes.

2013-03-21 | E-MTAB-1499 | biostudies-arrayexpress

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.

2019-08-01 | GSE118102 | GEO

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

Genome-wide analysis of PHABULOSA targets in Arabidopsis root meristem

Project description:We report the discovery of a root growth program in Arabidopsis that is independent of a functional quiescent center (QC). In this regulatory program, PHABULOSA (PHB), posttranscriptionally regulated by SHR and SCR, plays a central role. In phb shr and phb scr mutants, root meristem/growth activity recovers significantly. Interestingly, this recovery does not accompany the resurgence of QC cells. PHB regulates apical root growth in stele cells of the root meristem, located proximal to the QC. Our genome-wide investigation suggests that PHB exerts its influence on root growth by regulating auxin-cytokinin homeostasis. Apical root growth was restored when cytokinin levels were genetically reduced in the shr mutant. Conversely, when miRNA-resistant PHB was expressed in the root stele cells, apical root growth and meristem functions were significantly inhibited without blocking the QC identity. Taken together, our investigation reveals two mechanisms through which SHR regulates root growth and stem cell activities: one is to specify and maintain the QC and the other is to regulate the proximal meristem activity through PHB and cytokinin. In this regulation, QC seems to be more involved in maintaining the “growth signal” and thus ensure the indeterminate root growth.

2012-12-31 | GSE33015 | GEO

PHABULOSA controls the quiescent center-independent root meristem activities in Arabidopsis thaliana.

Project description: Not available

| S-EPMC4346583 | biostudies-literature

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

2013-11-04 | E-GEOD-48793 | biostudies-arrayexpress

RNAseq of germinal center B cells from Blimp-1-GFP reporter mice

Project description:RNAseq of germinal center B cells with different Blimp-1-GFP reporter level. Sorted germinal center populations were defined by their expression of Blimp-1-GFP reporter and the cell surface marker CD138 before they were further split into dark zone or light zone / dark zone like or light zone like cells based on their expression of the surface marker CXCR4 and CD83. We used RNAseq to find genes differentially regulated in various Blimp-1-GFP expressing germinal center populations from the spleen at day 10 after intraperitoneal immunisation with sheep red blood cells.

2018-12-20 | GSE111416 | GEO

Microarray transcriptomic profiling of Arabidopsis root stem cells within the BRL3 expression domain treated with Brassinolide (BL) [microarray]

Project description:Brassinosteroids (BRs) are steroid hormones involved in multiple processes of plant growth and development, and the adaptation to the environment. Some of the processes regulated by BRs are meristem activity and stem cell divisions. At the core of the root stem cell niche, it is placed the quiescent center (QC), that act as a cell reservoir. QC cells only trigger their divisions when need to replenish the stem cells, for example, after a DNA damage. BR signaling is in charge of triggering these QC divisions, but the exact mechanisms of how this process is regulated is still unknown. Here, we use an interdisciplinary approach, using Arabidopsis thaliana as a model system, including molecular genetics, physiology and bioinformatics to decipher the role of BR receptors upon DNA damage regulating the QC divisions. The results uncover novel roles for the BR-receptor kinase BRL3 (BRI1-like 3) receptor in DNA damage response (DDR) in plants, by modulating the DNA repair and the cell-cycle progression. We identified candidate tissue-specific transcriptional regulator, specifically expressed in the QC cells, the RNR2A (RIBONUCLEOTIDE REDUCTASE 2A), in charge of maintaining dNTPs (deoxynucleotide triphosphates) supply during DNA synthesis that is modulated by BRL3 downstream signaling events. Considering the importance of plant stem cells and their tissues for biomass accumulation and constantly exposed to adverse environmental stresses that can cause DNA damage or cell-cycle arrest in the RAM, here we stablished the mechanism linking root meristematic activity to the DDR through the cell-specific steroid receptor kinase BRL3.

2022-04-02 | GSE199742 | GEO

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