The SHR/SCR pathway directly activates genes involved in asymmetric cell division in the Arabidopsis root
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE15876 | GEO | 2010/07/19
SECONDARY ACCESSION(S): PRJNA117031
REPOSITORIES: GEO
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Project description:Asymmetric division of cortex/endodermal initials (CEI) in the Arabidopsis root generates two layers of ground tissue and is controlled by a finely orchestrated interplay between the transcription factors, SHORT ROOT (SHR) and SCARECROW (SCR). To understand the dynamics of the SHR/SCR regulatory network we performed microarray time course experiments using inducible versions of SHR and SCR and examined their transcriptional effects specifically in the ground tissue. Keywords: SHR and SCR time course and CEI cell-type analyses We performed a time course analysis (TC data set) of the ground tissue (sorted J0571 enancher trap) after transfer either SHR or SCR inducible plants to Dex containing plates 0, 1, 3, 6 and 12 hours. We sorted for CEI cells using the pCYCD6::GFP marker line. Seedlings were grown for 5 days. SHR and SCR inducible plants were transfer to 1microM Dex MS plates. J0571 and CYCD6 sorted fluorecent cells were harvested for RNA extraction.
2010-07-19 | E-GEOD-15876 | biostudies-arrayexpress
Project description:Transcriptional profiling of the vegetative part of Arabidopsis comparing wild type with the shr scl23 scr triple mutant. The latter is produced by crossing the strong null alleles of shr (shr-2), scl23 (scl23-1) and scr (scr-5). The goal was to determine the effects of the GRAS transcription factors SHR, SCL23 and SCR on growth and development of the Arabidopsis shoot system by global transcriptome analysis.
2012-10-11 | GSE41478 | GEO
Project description:Transcriptional profiling of the vegetative part of Arabidopsis comparing wild type with the shr scl23 scr triple mutant. The latter is produced by crossing the strong null alleles of shr (shr-2), scl23 (scl23-1) and scr (scr-5). The goal was to determine the effects of the GRAS transcription factors SHR, SCL23 and SCR on growth and development of the Arabidopsis shoot system by global transcriptome analysis. Two-condition experiment: Col-0 vs. shr scl23 scr triple mutant. Biological replicates: 2 WT vs. triple mutant replicates, 2 WT vs. triple mutant replicates dye-swap replicates.
2012-10-11 | E-GEOD-41478 | biostudies-arrayexpress
Project description:SHORT-ROOT (SHR) and SCARECROW (SCR) are required for stem cell maintenance in the Arabidopsis thaliana root meristem, ensuring its indeterminate growth. Mutation of SHR and SCR genes results in disorganization of the quiescent center and loss of stem cell activity, resulting in the cessation of root growth. This manuscript reports on the role of SHR and SCR in the development of leaves, which, in contrast to the root, have a determinate growth pattern and lack a persistent stem-cell niche. Our results demonstrate that inhibition of leaf growth in shr and scr mutants is not a secondary effect of the compromised root development, but is caused by a direct effect on cell division in the leaves: a reduced cell division rate and early exit of proliferation phase. Consistent with the observed cell division phenotype, the expression of SHR and SCR genes in leaves is closely associated with cell division activity in most cell types. The increased cell cycle duration is due to a prolonged S-phase duration, which is mediated by up-regulation of cell cycle inhibitors known to restrain the activity of the transcription factor, E2Fa. Therefore, we conclude that, in contrast to their specific role in cortex/endodermis differentiation and stem cell maintenance in the root, SHR and SCR primarily function as general regulators of cell proliferation in leaves.
2010-08-26 | GSE21629 | GEO
Project description:SHORT-ROOT (SHR) and SCARECROW (SCR) are required for stem cell maintenance in the Arabidopsis thaliana root meristem, ensuring its indeterminate growth. Mutation of SHR and SCR genes results in disorganization of the quiescent center and loss of stem cell activity, resulting in the cessation of root growth. This manuscript reports on the role of SHR and SCR in the development of leaves, which, in contrast to the root, have a determinate growth pattern and lack a persistent stem-cell niche. Our results demonstrate that inhibition of leaf growth in shr and scr mutants is not a secondary effect of the compromised root development, but is caused by a direct effect on cell division in the leaves: a reduced cell division rate and early exit of proliferation phase. Consistent with the observed cell division phenotype, the expression of SHR and SCR genes in leaves is closely associated with cell division activity in most cell types. The increased cell cycle duration is due to a prolonged S-phase duration, which is mediated by up-regulation of cell cycle inhibitors known to restrain the activity of the transcription factor, E2Fa. Therefore, we conclude that, in contrast to their specific role in cortex/endodermis differentiation and stem cell maintenance in the root, SHR and SCR primarily function as general regulators of cell proliferation in leaves. Total RNAs were extracted using RNeasy plant mini kit (Qiagen) from vegetative part of seedlings at stage 1.04 grown in vitro. RNAs from three biological repeats of wild type (wt, control) and scr and shr mutants were submitted to ATH1 array hybridization.
2010-08-26 | E-GEOD-21629 | biostudies-arrayexpress
Project description:ChIP-chip analysis was used to identify direct targets of the transcription factor SCR SCARECROW (SCR) is a key regulatory of radial patterning and stem cell renewal in the primary root. We have shown in previous studies that SCR is a direct transcriptional regulator in Arabidopsis thaliana. With the aim of understanding the molecular pathway acting downstream of SCR in primary root development, we identified SCR direct targets at the genome-wide level in primary roots.To do this we designed a promoter microarray (chip) for Arabidopsis containing probes tiling the intergenic regions, first intron, and 3’UTR of all annotated genes. We performed Chromatin Immunoprecipitation (ChIP) using an antibody to Green Fluorescent Protein (GFP) on roots of transgenic plants expressing a functional fusion protein of SCR and GFP that is driven by the SCR promoter. Our control was performing ChIP in parallel using the same anti-GFP antibody on roots of Columbia-O wild-type plants. DNA recovered from the SCR and wild-type ChIP experiments with Cy5 and Cy3 dye, respectively, and then hybridized to the same microarray. The array was scanned using an Agilent scanner and the signal intensity for each channel was retrieved and normalized by Agilent feature extraction software. Two biological replicates of this ChIP-chip experiment were performed.
2011-11-23 | GSE30104 | GEO
Project description:ChIP-chip analysis was used to identify direct targets of the transcription factor SCR SCARECROW (SCR) is a key regulatory of radial patterning and stem cell renewal in the primary root. We have shown in previous studies that SCR is a direct transcriptional regulator in Arabidopsis thaliana. With the aim of understanding the molecular pathway acting downstream of SCR in primary root development, we identified SCR direct targets at the genome-wide level in primary roots.To do this we designed a promoter microarray (chip) for Arabidopsis containing probes tiling the intergenic regions, first intron, and 3M-bM-^@M-^YUTR of all annotated genes. We performed Chromatin Immunoprecipitation (ChIP) using an antibody to Green Fluorescent Protein (GFP) on roots of transgenic plants expressing a functional fusion protein of SCR and GFP that is driven by the SCR promoter. Our control was performing ChIP in parallel using the same anti-GFP antibody on roots of Columbia-O wild-type plants. DNA recovered from the SCR and wild-type ChIP experiments with Cy5 and Cy3 dye, respectively, and then hybridized to the same microarray. The array was scanned using an Agilent scanner and the signal intensity for each channel was retrieved and normalized by Agilent feature extraction software. Two biological replicates of this ChIP-chip experiment were performed. Two biological replicates of the ChIP-chip experiment were performed using samples isolated from primary roots. Each Agilent array was hybridized with both SCR ChIP and wild-type control samples differentially labeled with Cy5 and Cy3 dye, respectively.
2011-11-23 | E-GEOD-30104 | biostudies-arrayexpress
Project description:A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and 166b. Endodermally produced miR165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage dependent manner. To investigate the global regulation of SHR and SCR in the root, direct and indirect target genes of SHR and SCR were cross-compared with selected cell type specific expression profiles in the Arabidopsis root published in Birnbaum et al. (2003), Nawy et al. (2005), Lee et al. (2006), and Brady et al. (2007) [pubmed IDs: 14671301, 15937229, 16581911, 17975066]. Furthermore, the mature endodermis specific transcript profiles were generated using a GFP marker line, E30, and used together with published profiles in this comparison.
2010-04-27 | E-GEOD-16469 | biostudies-arrayexpress
Project description:Hydrogen peroxide (H2O2) is a potent signaling molecule influencing various aspects of plant growth and development. Its limited lifetime and specific production sites in the plant cell necessitate the existence of specialized mechanisms that relay H2O2-encoded information. To discover such mechanisms, we focused on peroxisomal H2O2 production triggered by enhanced photorespiration in Arabidopsis mutants lacking catalase activity (cat2-2), and looked for second-site mutations that attenuate the negative effects (Fv'/Fm' decline and lesion formation) of H2O2 build up. A mutation residing in the GRAS family transcriptional regulator SHORT-ROOT (SHR) was found to underlie the increased performance of cat2-2 knock-outs under photorespiratory stress. In contrast to shr, introduction of the scr mutation in cat2-2 background did not improve the photorespiratory performance of plants lacking peroxisomal catalase. The absence of SHR negatively affected the activity of the photorespiratory enzymes glycolate oxidase and catalase, which was accompanied with elevated glycolate content and inability to accumulate glycine under conditions promoting photorespiration. The transcriptome signature of cat2-2 shr-6 double mutants exposed to photorespiratory stress lacked jasmonate-dependent signaling components, otherwise induced in cat2-2. The photorespiratory phenotype of cat2-2 was found to be modulated by exogenous sugars both in the presence and absence of shr. Taken together, these findings highlight a crucial role for SHR in H2O2 signal transduction and stress tolerance.
2016-06-10 | GSE66365 | GEO
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