Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA225782 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of overexpression of JMJ30 in Arabidopsis thaliana (Col). JMJ30 encode the histone demethylases that contain the catalytic JmjC domain. The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. Here, we show that JMJ30 encodes a H3K27me3 demethylase, and genes up-regulated in 35S::JMJ30-HA transgenic lines are enriched for H3K27me3 targets. Columbia wild-type (Col WT) and 35S::JMJ30-HA transgenic plants were grown at 22°C under long day conditions, and seedling samples were collected at 13 day-after-germination (DAG). Two independent sets of WT and 35S::JMJ30-HA seedling mRNA samples were used for this array.
2014-08-31 | E-GEOD-51896 | biostudies-arrayexpress
Project description:To determine the role of HY5 under HL in transcriptional regulation, RNA-seq was performed on 7-day-old Col-0 and hy5 mutant seedlings grown under GL and HL conditions. HY5-dependent and HL-responsive differentially expressed genes (DEGs) were identified by comparing Col-0 vs. hy5 under HL, and GL vs. HL conditions, respectively (Fig. S8A). Using a 2-fold change and p ≤ 0.05 cutoff, 6,929 and 7,378 DEGs were detected in Col-0 and hy5, respectively, with 4,130 genes overlapping (Fig. S8B). Volcano plot analysis identified 615 upregulated and 291 downregulated HY5-dependent genes under HL. Next, transcriptome analysis was conducted using RNA-seq on 7-day-old seedlings of Col-0, hy5, 35S:HY5K87K-GFP/hy5#1, 35S:HY5K87Q-GFP/hy5#1, and 35S:HY5K87R-GFP/hy5#2 grown under GL conditions. Comparison of DEGs between transgenic lines and the hy5 mutant revealed 3,755, 3,450, 5,341, and 5,935 upregulated, and 4,139, 3,584, 5,832, and 6,209 downregulated genes in Col-0 (native HY5), 35S:HY5K87K-GFP/hy5#1 (HY5K87K), 35S:HY5K87Q-GFP/hy5#1 (HY5K87Q), and 35S:HY5K87R-GFP/hy5#2 (HY5K87R) seedlings, respectively.
2026-01-05 | GSE308603 | GEO
Project description:ChIP-Seq were performed using 35S::GFP-ASF1A, pHTR13::HTR13-HA, pHTR5::HTR5-HA, and pHTR5::HTR5-HA/pif7-1 transgenic plants after white light and 1 hr shade treatment. Two biological replicates were prepared for each genotype of plants grown under light and shade conditions. High-confidence binding peaks with cut off fold change > 1.5 and P-value <0.01. Our data reveal that ASF1 directly regulating a subset of target genes of PIF7. Furthermore, shade-elicited gene activation is accompanied by H3.3 enrichment, which is mediated by the PIF7-ASF1 regulatory module.
2023-01-30 | GSE193955 | GEO
Project description:Two independent Solanum tuberosum ssp. Andigena ADG StCEN RNAi and two ADG StCEN 35S overexpressing OE transgenic lines and a wild type WT control were grown under standard glasshouse conditions for 6 weeks prior to being moved to controlled growth cabinet conditions. Plants were grown under 4 different daylengths (8,10,12 and 16 hr) at 20 °C day and 14 °C night temperatures. ADG StCEN RNAi lines showed signs of early tuberization phenotype compared with the WT control after 23 days in the cabinets. Non-swelling stolons were harvested at this timepoint. ADG StCEN 35S OE lines demonstrated a delayed tuberization phenotype compared with the WT control. Non-swelling stolons were harvested after 38 days in the controlled cabinet conditions.
2020-07-01 | E-MTAB-8346 | biostudies-arrayexpress
Project description:In this study we analyzed the effect of overexpression of an HA-tagged version of the ERF RAP2.12 on the transcriptome levels in aerobic and hypoxic-treated (O2 21% and 1%, respectively) Arabidopsis thaliana rosettes. We also analyzed the effect of a RAP2.12 and RAP2.2 simultaneous silencing in aerobic and hypoxic-treated (O2 21% and 1%, respectively) Arabidopsis thaliana rosettes. We treated Arabidopsis Col-0 (wt) rosettes and transgenic HA::RAP2.12 and amiRAP2.2-12 , 5-week old, grown in 8/16 light/dark photoperiod with: -Control (22°C, dark, 21% O2, 1.5h). -Hypoxia (22°C, dark, 1% O2, 1.5h).
2011-10-13 | E-GEOD-29187 | biostudies-arrayexpress
Project description:Analysis of overexpression of JMJ30 in Arabidopsis thaliana (Col). JMJ30 encode the histone demethylases that contain the catalytic JmjC domain. The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. Here, we show that JMJ30 encodes a H3K27me3 demethylase, and genes up-regulated in 35S::JMJ30-HA transgenic lines are enriched for H3K27me3 targets.
2014-08-31 | GSE51896 | GEO
Project description:We used whole-genome microarrays to identify differentially expressed genes in leaves of GA-deficient (35S::PcGA2ox) and/or GA-insensitive (35S::rgl1) transgenics as compared to WT poplar (717-1B4 genotype). Our work suggests that the molecular machinery that reduces gibberellins (GAs) concentration and signaling is a major route for restraining growth under both immediate and imminent adverse conditions. We show that inhibition of growth as a result of water deprivation and short days (SDs) coincides with up-regulation of several DELLA and GA2ox encoding genes in poplar. Likewise, GA-deficient and GA-insensitive transgenics, with up-regulated GA2ox and DELLA domain proteins, elicited a hypersensitive growth inhibition in response to both drought and SDs. Because the GA-modified transgenic showed accelerated response to drought and SD, we hypothesized that the mechanisms associated with these responses are constitutively elevated even under control conditions (well-watered, long day photoperiod). Therefore, we used whole-genome poplar microarray to study transcriptome level changes in the leaves of transgenic compared to WT plants grown under control environment.
2014-01-01 | GSE38390 | GEO
Project description:The timing of many molecular and physiological processes in plants occurs at a specific time of day. The circadian MYB-like transcription factor REVEILLE 8 (RVE8) interacts with its transcriptional coactivators NIGHT LIGHT INDUCIBLE AND CLOCK REGULATED 1 (LNK1) and LNK2 to promote the expression of evening-phased clock genes and cold tolerance factors. While genetic approaches have commonly been used to discover new connections within the clock and between other pathways, here we use affinity purification coupled with mass spectrometry to discover time-of-day-specific protein interactors of the RVE8-LNK1/2 complex. Our clock proteins are tagged with a 6X-His-3X-FLAG C-terminal (HFC) affinity tag and purified through anti-FLAG immunoprecipitation and His-tag isolation affinity purification. We also performed affinity purification-mass spectrometry of 35S::YFP-COR27 and 35S::GFP-COR28, which were immunoprecipitated with anti-GFP TRAP beads. Experiment was performed on 10-day-old seedlings grown under 12 hours light: 12 hours dark 22 degrees Celsius.
2023-04-24 | PXD034089 | Pride
Project description:Promoters of many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. A least three R1R2R3-Myb proteins are expressed in tobacco (Nicotiana tabacum). To examine the genome-wide effects of NtmybA2 overexpression, we constructed transgenic tobacco BY-2 cell lines overexpressing full-length NtmybA2 protein. In addition, we generated transgenic BY-2 cell lines that overexpress truncated hyperactive form of NtmybA2 (NtmybA2âC) lacking its C-terminal region which negatively regulates its own activity for transcriptional activation. We used a custom-made 16K cDNA microarray for comparative transcriptome analysis of these transgenic tobacco BY-2 cell lines. As control sample, BY-2 cells transformed with empty vector pPZP-35S were used. The transgenic cell lines were analyzed during stationary phase (i.e. day 7-8 after subculture into fresh media). Keywords: Genetic modification 1. pPZP-35S vector control, 2. NtmybA2 overexpressor, 3. C-truncated NtmybA2 (NtmyA2âC) overexpressor
2010-05-22 | E-GEOD-14251 | biostudies-arrayexpress
Project description:Transcription profiling of wild type and transgenic 35S:PAR1-GG seedlings. To characterize the transcriptional networks altered by constitutive overexpression of PAR1 in seedlings, using two-color long-oligonucleotide microarrays.
2007-11-03 | E-ATMX-29 | biostudies-arrayexpress