The transcriptome analysis of WUS targets
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE128778 | GEO | 2021/02/22
REPOSITORIES: GEO
Similar Datasets
Project description:Cell-cell communication is critical for stem cell maintenance. Shoot apical meristem (SAM) located at the shoot tip harbors stem cells within the central zone (CZ). Their progeny differentiate in the adjacent peripheral zone (PZ). WUSCHEL (WUS) is a homeodomain transcription factor produced in a few cells of the organizing center (OC), located beneath the CZ. It has been shown to specify stem cell fate and also activate CLAVATA3 (CLV3) expression in cells of the CZ. CLV3 is a secreted peptide that activates a membrane bound receptor kinase-CLAVATA1 to restrict WUS transcription to the OC. It has been hypothesized that WUS activates CLV3 expression and stem cell fate in adjacent cells of the CZ by activating a non-cell autonomous signal. Contrary to this hypothesis, here we show that the WUS protein after being synthesized in cells of the OC, migrates into the superficial cell layers of the CZ where it activates CLV3 transcription by binding to its promoter elements. WUS also migrates laterally into the PZ to repress the expression of differentiation promoting transcription factors by binding to their regulatory regions. Migration of a stem cell inducing transcription factor into adjacent cells to activate a negative regulator, whereby restricting its own accumulation is unique to plant stem cell niches. While stem cell promoting transcription factor directly repressing differentiation promoting transcription factors to prevent premature differentiation of stem cell progenitors is conserved among diverse stem cell niches. A dexamethasone inducible version of WUSCHEL was used to identify its direct tragets. To analyze WUS-regulated gene expression programs at a higher spatial resolution, we introduced a dexamethasone (Dex)-inducible form of WUS consisting of the WUS protein-coding region fused to sequences coding for the ligand-binding domain of the rat glucocorticoid receptor (GR), expressed under a ubiquitous promoter (35S::WUS-GR) into apetala1-1;cauliflower1-1 (ap1-1;cal1-1) double mutant background. 35S::WUS-GR; ap1-1;cal1-1 SAMs were either treated with 10μM Dex or mock solution for four hours and RNA samples were hybridized to Arabidopsis ATH1 gene Chip (Affymmetrix). To identify putative genes that are directly regulated by WUS, in independent experiments, SAMs were simultaneously treated with 10μM Dex and 10μM Cycloheximide (Cyc), protein synthesis inhibitor and Cyc alone for four hours. A comparison of Dex-treated samples with mock identified 641 genes as differentially expressed [DEGs] (≥/≤2 fold; p < 0.01) and comparison of Dex+Cyc with Cyc identified 457 genes as DEGs (≥/≤2 fold; p < 0.01).
2013-03-26 | E-GEOD-29364 | biostudies-arrayexpress
Project description:9-day-old jaw-D;pTCP4::mTCP4:GR treated with Cycloheximide (CHX, control) and the combination of Cycloheximide and Dexamethasone (CHX DEX, treated).
2021-05-20 | GSE174702 | GEO
Project description:Cell-cell communication is critical for stem cell maintenance. Shoot apical meristem (SAM) located at the shoot tip harbors stem cells within the central zone (CZ). Their progeny differentiate in the adjacent peripheral zone (PZ). WUSCHEL (WUS) is a homeodomain transcription factor produced in a few cells of the organizing center (OC), located beneath the CZ. It has been shown to specify stem cell fate and also activate CLAVATA3 (CLV3) expression in cells of the CZ. CLV3 is a secreted peptide that activates a membrane bound receptor kinase-CLAVATA1 to restrict WUS transcription to the OC. It has been hypothesized that WUS activates CLV3 expression and stem cell fate in adjacent cells of the CZ by activating a non-cell autonomous signal. Contrary to this hypothesis, here we show that the WUS protein after being synthesized in cells of the OC, migrates into the superficial cell layers of the CZ where it activates CLV3 transcription by binding to its promoter elements. WUS also migrates laterally into the PZ to repress the expression of differentiation promoting transcription factors by binding to their regulatory regions. Migration of a stem cell inducing transcription factor into adjacent cells to activate a negative regulator, whereby restricting its own accumulation is unique to plant stem cell niches. While stem cell promoting transcription factor directly repressing differentiation promoting transcription factors to prevent premature differentiation of stem cell progenitors is conserved among diverse stem cell niches. A dexamethasone inducible version of WUSCHEL was used to identify its direct tragets.
2013-03-26 | GSE29364 | GEO
Project description:We used a systems approach to identify target genes and genome wide chromatin binding preferences of the transcription factor WUSCHEL (WUS) in Arabidopsis thaliana. First, we recorded changes in the transcriptome after genetically perturbing the regulatory system of the stem cell niche at various developmental stages by loss-of-function and inducible over-expression alleles of WUS and its antagonist CLV3. Then, identified direct WUS target genes by chromatin immuno-precipitation (ChIP.
2010-06-01 | E-MEXP-2499 | biostudies-arrayexpress
Project description:A glucocorticoid-regulated BBM protein (35S:BBM-GR) was used in combination with microarray analysis to identify genes directly activated by BBM. We employed the system described by (Lloyd et al., 1994) in which dexamethasone (DEX) and cycloheximide (CHX) are applied together to respectively, induce nuclear localization of the BBM-GR protein and prevent translation of the primary targets mRNAs. In this way it is possible to identify direct targets of a transcriptional activator by comparing gene expression profiles between DEX+CHX-treated transgenic and wild-type tissues. The ability of the 35S:BBM GR construct to induce somatic embryogenesis in Arabidopsis seedlings was determined by phenotypic observation of 35S:BBM GR seeds germinated and grown in the presence of 10 µM dexamethasone (DEX). As in 35S:BBM seedlings, we observed somatic embryo formation on the cotyledons, first leaves and shoot meristem of DEX-treated 35S:BBM GR seedlings. We identified a set of 20 genes (including BBM itself) and our analysis indicates that BBM directly activates a signaling pathway comprising transcription factors and other signaling molecules, but which does not initially include genes known to induce somatic embryogenesis, such as LEC1, LEC2 or WUS. The functions of the BBM target genes are unknown, however a number of them have recently been identified in microarray screens for meristem-expressed genes. The identification of BBM-interacting partners and downstream targets provides new tools for unraveling pathways related to plant cell growth and organogenesis. Keywords: transcriptional activation
2008-09-22 | GSE3399 | GEO
Project description:Direct target genes of VND7 were explored with inducible expression system using glucocorticoid receptor (GR). Transgenic plants expressing 35S:VND7-VP16-GR were treated with dexamethazone (DEX) and/or protein synthesis inhibitor cycloheximide (CHX). A number of genes related to the formation of vascular vessel was induced by DEX even in the presence of CHX. Total RNAs of the transgenic plants expressing 35S:VND7-VP16-GR treated with DEX plus CHX and those treated with CHX only were compared. As a control experiment, transgenic plants harboring empty vector were treated similarly and the total RNAs were compared similarly to identify genes merely induced by DEX treatment itself.
2011-03-31 | E-GEOD-24169 | biostudies-arrayexpress
Project description:Global expression of the Arabidopsis transcriptional regulator SHOOT MERISTEMLESS (STM) in a 35S:STM-GR transgenic line was induced for 3 hours with dexamethasone (DEX) compared to mock-induced (DMSO) control. Additionally,to identify direct targets, plants were treated with the protein synthesis inhibitor cycloheximide (CHX) together with DEX, compared to CHX treatment alone.
2018-05-29 | E-MTAB-6786 | biostudies-arrayexpress
Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone or dexamethasone+cycloheximide treatment. Tissue samples were collected at 3hrs after the treatment. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (Agilent, custom-commercial). We treated inflorescences of 35S:AP1-GR ap1-1 cal-1 plants with a dexamethasone-containing or a mock solution, or with identical solutions that contained in addition 10 M-NM-<M cycloheximide. Tissue was collected 3 hours after the treatment. Samples from each of the four biological replicates resulted in a set of four hybridization pairs: Mock vs. Dex, Mock vs. Chx, Mock vs. Dex+Chx, and Chx vs. Dex+Chx. Dye polarities were switched between biological replicates.
2011-01-01 | E-GEOD-20175 | biostudies-arrayexpress
Project description:Maintenance and regulation of the shoot apical meristem size and boundaries are essential for plant growth and leaf organogenesis. Canonically, CLAVATA 1, CLAVATA 3 and WUSCHEL control shoot apical meristem (SAM) size and SAM maintenance. Recently it has been shown that ERECTA (ER) family genes also control SAM size at its boundaries. The ERECTA family of receptor like protein kinases are bound by EPIDERMAL PATTERNING FACTOR LIKE (EPFL) protein ligands. Loss of the ER receptor genes or a subset of the EPFL ligands lead to an enlarged meristem. Loss of both CLAVATA genes and ER family genes synergize to produce even larger meristems with a loss of leaf production. In this experiment we perform deep sequencing to measure the transcriptome wide molecular changes in the clv3 epfl1 epfl2 epfl4 epfl6 quintuple mutant under mock, 3h ectopic EPLF6 ligand, 10 minute pretreatment with cycloheximide (CHX) and combined 10 minute CHX pretreatment followed by a 3h EPFL6 treatment. Treatment of the quintuple mutant with EPFL6 leads to a modest but targeted downregulation of MEI2 C-TERMINAL RRM ONLY LIKE 1(MCT1) RNA binding family proteins. CHX treatment was used to inhibit the translation of new proteins. By blocking new protein production, only direct signaling targets of EPFL6 would be seen. The severe toxic effects of CHX leads to a complete rearrangement of the transcriptome. However, EPFL6 still alters some CHX targets, mostly through downregulation.
2024-06-10 | GSE243494 | GEO
Project description:A glucocorticoid-regulated BBM protein (35S:BBM-GR) was used in combination with microarray analysis to identify genes directly activated by BBM. We employed the system described by (Lloyd et al., 1994) in which dexamethasone (DEX) and cycloheximide (CHX) are applied together to respectively, induce nuclear localization of the BBM-GR protein and prevent translation of the primary targets mRNAs. In this way it is possible to identify direct targets of a transcriptional activator by comparing gene expression profiles between DEX+CHX-treated transgenic and wild-type tissues. The ability of the 35S:BBM GR construct to induce somatic embryogenesis in Arabidopsis seedlings was determined by phenotypic observation of 35S:BBM GR seeds germinated and grown in the presence of 10 µM dexamethasone (DEX). As in 35S:BBM seedlings, we observed somatic embryo formation on the cotyledons, first leaves and shoot meristem of DEX-treated 35S:BBM GR seedlings. We identified a set of 20 genes (including BBM itself) and our analysis indicates that BBM directly activates a signaling pathway comprising transcription factors and other signaling molecules, but which does not initially include genes known to induce somatic embryogenesis, such as LEC1, LEC2 or WUS. The functions of the BBM target genes are unknown, however a number of them have recently been identified in microarray screens for meristem-expressed genes. The identification of BBM-interacting partners and downstream targets provides new tools for unraveling pathways related to plant cell growth and organogenesis. Keywords: transcriptional activation To identify candidate BBM targets, we treated 4 day old 35S:BBM-GR seedlings for 8 hours with 10 µM DEX in the presence of 10 µM CHX and compared the mRNA population from these seedlings using Arabidopsis Operon microarrays (http://www.ag.arizona.edu/microarray/) to that of 4 day old wild-type seedlings treated in the same way. The seed batches used in this analysis showed 100% EFS when grown continuously on media with 10 µM DEX. Four day old seedlings were chosen as the experimental material because they are highly responsive to BBM GR activation and provide sufficient RNA for the microarray experiments. The biological reproducibility of the data was monitored using two independent single locus 35S:BBM GR lines. The technical reproducibility of the data was monitored using two independently DEX + CHX-treated samples from each transgenic line. Dye effects were monitored in a dye-swap experiment using one of the four RNA samples from the two biological replicates
2010-06-25 | E-GEOD-3399 | biostudies-arrayexpress