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Identification of ORB1 target genes using inducible overexpression system

ABSTRACT: The aim was to identify genes associated to the down-regulation TARGET OF RAPAMYCIN (TOR) pathway in Arabidopsis. For this purpose, three independent amiR-tor lines (amiR-tor9, amiR-tor17 and amiR-tor 20) and EV lines 3 and 6 days after EST- or non-induction were used for expression profile analysis using Affymetrix microarray. Two weeks-old transgenic seedlings were transferred to MS plate with 20µM estradiol to induce the overexpression of amiR-tor (consequently, repression of AtTOR levels) under the control of an estradiol-(EST) inducible promoter. Identically treated wild-type Col-0 and pER8 empty-vector (EV) transformed seedlings were served as controls. Seedlings were harvested after 3 and 6 (amiR-tor lines) days.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE38878 | GEO | 2013/01/31

SECONDARY ACCESSION(S): PRJNA169133

REPOSITORIES: GEO

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Identification of ORB1 target genes using inducible overexpression system

Project description:The aim was to identify genes associated to the down-regulation TARGET OF RAPAMYCIN (TOR) pathway in Arabidopsis. For this purpose, three independent amiR-tor lines (amiR-tor9, amiR-tor17 and amiR-tor 20) and EV lines 3 and 6 days after EST- or non-induction were used for expression profile analysis using Affymetrix microarray. Two weeks-old transgenic seedlings were transferred to MS plate with 20ÂµM estradiol to induce the overexpression of amiR-tor (consequently, repression of AtTOR levels) under the control of an estradiol-(EST) inducible promoter. Identically treated wild-type Col-0 and pER8 empty-vector (EV) transformed seedlings were served as controls. Seedlings were harvested after 3 and 6 (amiR-tor lines) days. genetic modification

2013-01-31 | E-GEOD-38878 | biostudies-arrayexpress

Genome wide analysis of the chromatin state and gene expression in Wild-type, tor-es mutant, and fie mutants

Project description:Using Western blot, we found the level of H3K27me3, but not H3K4me3, H3K9me2 and H3K36me3, was specifically reduced in the tor-es mutant. To gain a genome-wide view of the effects of TOR activity on H3K27me3 distribution, we performed quantitative chromatin immunoprecipitation with an exogenous reference genome (ChIP-Rx) followed by deep-sequencing. We find a global reduction of H3K27me3 occupancy in tor-es, whereas the H3K9me2 level was largely unaffected. These results suggest that TOR may be a specific and direct regulator of global deposition of H3K27me3. To investigate the function of TOR phosphorylation of FIE, we complemented the heterozygous fie/+ plants with GFP-FIE or the phosphorylation site mutant (SSTS/AAAA) under the control of the FIE promoter. To provide a parallel comparison with SSTS/AAAA/fie, we generated estradiol-inducible fie-amiR-es transgenic lines, that eliminated FIE protein. Quantitative ChIP-seq analyses revealed greatly reduced H3K27me3 levels across the genome in SSTS/AAAA and fie-amiR-es mutants. And transcriptome profiling by RNA-Seq was conducted to globally identify thousands of genes coordinately dysregulated in the shoots of SSTS/AAAA and fie-amiR-es plants. Furthermore, gene Ontology analysis of 986 TOR-FIE-PRC2 target genes revealed significant enrichment for transcription factors/regulators controlling a broad spectrum of developmental programs.

2022-06-20 | GSE161807 | GEO

Coordinate transcriptional activation of salicylic acid and trehalose synthesis, oxidative/ER stress and innate immunity pathways by inducible artificial microRNA silencing of the SNF4 activator subunit of Arabidopsis SnRK1

Project description:Arabidopsis SnRK1 is structurally and functionally related to the yeast Snf1 and mammalian AMP-activated kinases, which are activated in response to carbon/glucose limitation and stress conditions causing an imbalance of energy homeostasis increasing the AMP/ATP ratio. Mutations of the SNF4 activating subunit of trimeric Arabidopsis SnRK1 complexes are not transmitted through the male meiosis. Silencing of SNF4 by a β-estradiol-inducible artificial microRNA (amiR-SNF4) constructs was used to examine how inhibition of SnRK1 affects transcriptional regulation of different cellular pathways in dark and light grown seedlings. This study shows that amiR-SNF4 silencing of SnRK1 leads to coordinate transcriptional activation of salicylic acid and trehalose synthesis, oxidative/endoplasmic reticulum stress and pathogen defense responses by inducing simultaneous changes in numerous other essential hormonal and metabolic pathways in Arabidopsis. We used Affymetrix ATH1-121501 Genome Array to compare global transcript levels in wild type and β-estradiol-induced amiR-SNF4 mutant seedlings 5 days after germination in the dark or light.

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2019-01-01 | GSE100654 | GEO

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2013-04-05 | E-GEOD-40245 | biostudies-arrayexpress

Genome wide expression analysis of EST-induced EBE-XVE using Affymetrix ATH1 array

Project description:Global transcriptome patterns were determined in XVE-14 and wild-type seedlings induced for 45 min b-estradiol in order to identify the genes early regulated by EBE transcription factor. We used microarrays to identify genes differentially expressed in EST-inducible EBE over-expression line #14 compared to wild-type plants, 45 min after 2µM EST induction. Three independent biological replications were performed.

2013-03-30 | GSE27855 | GEO

transcriptomic analysis of phosphatin effect-Phosphatin effect on Arabidopsis

Project description:cea11-02_phosphatin - transcriptomic analysis of phosphatin effect - Identification of transcriptomic modifications promoted by phosphatin (AC6) (a molecule mimicking Pi addition effects on Pi starved plants). - 40 µM Phosphatin was added to MS (diluted 10 times) containing 20µM phosphate medium and controls were grown on MS (diluted 10 times) containing 20µM phosphate or supplemented with 500 µM of Pi. For each ARN extraction their was 3 plates containing each 10 seedlings grown 13 days in vertical petri dishes.

2013-04-11 | GSE45937 | GEO

Transcriptome profiling of Arabidopsis roots upon lateral root induction in WT and TOR knock down [dataset1]

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2022-03-23 | GSE199202 | GEO

Genome wide expression analysis of EST-induced MYB112 (MYB112-IOE) using Affymetrix ATH1 array

Project description:Global transcriptome patterns were determined in MYB112-IOE seedlings induced for 3 h and 5 h with b-estradiol in order to identify the genes early regulated by MYB112 transcription factor. We used microarrays to identify genes differentially expressed in EST-inducible MYB112 over-expression line #1, 3 h and 5 h after 10µM EST induction, compared to mock treated plants. Two independent biological replications were performed for 5 h timepoint and one replicate for 3 h timepoint.

2015-11-03 | GSE36721 | GEO

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