Identification of WRKY22 targets under submergence in Arabidopsis
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Fu-Chiun Hsu
PROVIDER: E-GEOD-40140 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:To identify direct targets of WRKY22, we created a transgenic Arabidopsis line that expresses a c-myc epitope-tagged WRKY22 and used ChIP followed by microarray hybridization (ChIP-chip) to screen for candidates and validate the in vivo protein-DNA interactions with ChIP followed by quantitative PCR (ChIP-Q-PCR). The WRKY22 and c-myc epitope tag fusion construct was generated and transformed into wrky22-ko2 plants. The resulting transgenic lines should have better ChIP efficiency than the wild-type background, due to the reduced competition for WRKY22 binding sites from endogenous WRKY22. ChIP-enriched DNA fragments were identified using criteria of a window of +300 to M-oM-<M-1200 of a gene for a promoter, a width of 4 probes or more, and a false discovery rate (FDR) < 0.1. The ChIP-chip experiments were repeated six times, i.e., six biological replicas. Candidates were defined by the presence of the promoter in three out of six biological replicas. Candidates were then classified based on their hypoxic responsiveness with a positive response defined as gene expression levels exhibiting > 2 or < 0.5-fold induction in any time point under submergence treatments in expression array data. Comparison of c-myc tagged WRKY22 transgenic plants vs wild-type (Columbia) plants. Both materials were submergence treated for 3 hours.
2013-07-03 | E-GEOD-40138 | biostudies-arrayexpress
Project description:We analyzed global transcriptional changes in both shoots and roots of root-flooded Arabidopsis seedlings by microarrays. We also interpreted the significance of the systemic communication between roots and shoots by functional classification of affected genes. We performed genetic analysis with an ethylene signaling mutant, ein2-5, to correlate systemic flooding responses with ethylene signaling. We identified a class of genes that were up- or downregulated in shoots, but not affected in roots, under hypoxic conditions. A comprehensive managing program of carbohydrate metabolism was observed, providing an example of how systemic communications might facilitate the survival of plants under flooding. A proportion of long-distance hypoxic regulation was altered in ein2-5. Time course experiments (0.5, 1, 3, 6, and 12h for Columbia; 0.5, 3, and 6h for ein2-5). Tissues from root-flooded seedlings vs. Tissues from un-flooded seedlings. Biological replicates: 4 replicates for each time point, independently grown, treated, and harvested. One replicate per array. 2 of 4 replicates are dye-swapped.
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Project description:To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs, high-throughput sequencing Amplicons were prepared by 5' and 3' adaptor ligation and RT-PCR using small RNA fractions from inflorescence tissue (containing stage 1-12 flowers) of wt Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), and mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15). Amplicons from whole seedlings (3 day post-germinations) were prepared from Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.
2007-02-01 | E-GEOD-6682 | biostudies-arrayexpress
Project description:We analyzed global transcriptional changes in submerged Arabidopsis seedlings comparing control untreated seedlings. The same analysis were also applied on wrky22-ko2 seedling to identify WRKY22 targets under submergence. Time course experiments (1, 3, and 6 for Columbia and wrky22-ko2). Tissues from submerged seedlings vs. Tissues from un-submerged seedlings. Biological replicates: 4 replicates for each time point, independently grown, treated, and harvested. One replicate per array. 2 of 4 replicates are dye-swapped.
2013-07-03 | E-GEOD-40139 | biostudies-arrayexpress
Project description:Arabidopsis thaliana AF7/ARF19 double knockout with ARF7 reintroduced under its own promotor with a glucocorticoid receptor added were treated with Auxin, Dexamethazone and cycloheximide to determine primary and secondary ARF7 auxin sensitive downstream targets
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Project description:Accumulation of unfolded/misfolded proteins in endoplasmic reticulum (ER) elicits a well conserved response called the Unfolded Protein Response (UPR), which triggers the up-regulation of downstream genes involved in protein folding, vesicle trafficking, and ER-Associated Degradation (ERAD). Although the dynamic transcriptomic responses and underlying major transcriptional regulators in ER stress response in plants have been well established, the proteome changes induced by ER stress have not been reported in plants. In the current study, we found that the Arabidopsis Ler ecotype is more sensitive to ER stress than the Col ecotype. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that totally 7439 and 7035 proteins were identified from Col and Ler seedlings, with 88 and 113 differentially regulated (FC>1.3 or <0.7, P<0.05) proteins by ER stress in Col and Ler, respectively. Among them, 40 proteins were commonly up-regulated in Col and Ler, of which 10 were not up-regulated in bzip28 bzip60 double mutant (Col background) plants. Of the 19 specifically up-regulated proteins in Col comparing to that in Ler, components in ERAD, N-glycosylation, vesicle trafficking and molecular chaperones were represented. Quantitative RT-PCR showed that genes encoding 7 out of 19 proteins were not up-regulated (FC>1.3 or <0.7, P<0.05) by ER stress in both ecotypes while genes encoding 12 out of 19 proteins were up-regulated by ER stress with no obvious differences in fold change between Col and Ler. Our results experimentally demonstrated the robust ER stress response at proteome level in plants and revealed differentially regulated proteins that may contribute to differed ER stress sensitivity between Col and Ler ecotypes in Arabidopsis.
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Project description:Many of duplicated genes are enriched in signaling pathways. Recently, gene duplication of kinases has been shown to provide genetic buffering and functional diversification in cellular signaling. Transcription factors (TFs) are also often duplicated. However, how duplication of TFs affects their regulatory structures and functions of target genes has not been explored at the systems level. Here, we examined regulatory and functional roles of duplication of three major ARR TFs (ARR1, 10, and 12) in Arabidopsis cytokinin signaling using wild-type and single, double, and triple deletion mutants of the TFs. Comparative analysis of gene expression profiles obtained from Arabidopsis roots in wild-type and these mutants showed that duplication of ARR TFs systematically extended their transcriptional regulatory structures, leading to enhanced robustness and diversification in functions of target genes, as well as in regulation of cellular networks of target genes. Therefore, our results suggest that duplication of TFs contributes to robustness and diversification in functions of target genes by extending transcriptional regulatory structures. Duplication of TFs can confer an extension of transcriptional regulatory structures for target genes by providing new regulatory relationships between duplicated TFs and new or old target genes. To examine the nature of the extension in the regulatory structure, we performed gene expression profiling of Arabidopsis root tissues obtained from wild-type (WT) and deletion mutants of three type-B ARR1, 10, and 12. To examine how the extended regulatory structures by the duplicated ARR TFs are utilized for the responses to external CK, we generated gene expression profiles of WT Arabidopsis roots treated with mock or exogenous CK for 1 hour. Total RNAs were isolated from two biological replicates at each condition and used to measure gene expression level.
2015-02-03 | E-GEOD-62597 | biostudies-arrayexpress
Project description:In plants, formation of functional stomatal guard cells is a highly regulated event so that this cell differentiation model constitutes an interesting genetic system to explore cell differentiation in response to cell cycle controllers or cell fate determinants such as transcription factors. The latest acting bHLH in the stomatal lineage circuit is FAMA that appears to be absolutely required to promote stomatal development by controlling the GMC to GC transition. In order for FAMA to trigger guard cell development, it probably initiates a gene activation cascade leading to cell differentiation and cessation of cell division. To identify and characterize FAMA inducible genes, transcriptome analysis using the Affymetrix ATH1 micro-array chip was carried out on inducible FAMA gain of function plants at 4hrs and 48 hrs post-induction. Transgenic plants with an estrogen-inducible FAMA expression cassette were used in a timecourse experiment to identify genes that were differentially regulated by FAMA. Two time points were analyzed, 4 hours and 48 hours post-induction. Seedlings were grown on vertically oriented plates in a 22 °C incubator under 24 hours light for 5 days. Plants were then transfered with forcepts to plates containing MS + Sucrose + 10 µM estrogen (or new MS + sucrose plates for controls). After 4h or 48h on new plates, samples were collected, frozen in liquid nitrogen and stored at â??80 degree until enough material was obtained to do all RNA extractions in the same week. The Rneasy Plant Mini Kit (QIAGEN) for RNA isolation, and samples were labelled with standard kits, etc (get info) and hybridized to Affymetrix Ath1 array chips. 15 samples.
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