Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Title: Lysine acetylation modulates HY5 function in Arabidopsis under high light conditions

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE308603 | GEO | 2026/01/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The interactome of histone deacetylase HDA19 in dark-grown Arabidopsis seedlings

Project description:In this Data Report, we provide an immunoprecipitation (IP)-based analysis of the HDA19 interactome in etiolated Arabidopsis seedlings. We believe that the interactome presented here provides a valuable resource for follow-up research on novel interacting partners of this central protein. The material used for this experiment was derived from hypocotyls of 6-day-old etiolated Arabidopsis seedlings. The dataset contains a total of 6 files, 3 independent biological replicates of each Col-0 (control plants) and 35S::HDA19-GFP plants.

2023-09-19 | PXD045454 | Pride

Identify BZR1 interactome by IP-MS in Arabidopsis

Project description:we performed stable isotope labeling followed by Immunoprecipitation and quantitative MS (SILIP-MS) with Arabidopsis seedlings 35S:BZR1-YFP/Col-0 and Col-0.

2024-07-11 | PXD043666 | JPOST Repository

Temporal analysis of physiological and transcriptome responses during high light exposure that lead to dynamic acclimation in Arabidopsis

Project description:The photosynthetic capacity of mature leaves increases upon exposing plants to continuous or intermittent high light (HL). This is termed dynamic acclimation, which is an important determinant of plant productivity. We hypothesized that genes coding for transcription regulators (TRs), which respond rapidly (≤1h) and transiently to HL, initiate dynamic acclimation. To find such genes, a highly replicated time series transcriptomic dataset was generated from leaf 7 of low light (LL)-grown Arabidopsis thaliana plants subjected to HL for up to 6h. This revealed 3844 HL-responsive differentially expressed genes (DEGs). 49 transiently HL-induced TR DEGs were selected for Bayesian modeling, which revealed that B-BOX TRANSCRIPTION (CO) FACTOR32 (BBX32) was the most connected gene in an inferred network. Dynamic acclimation was elicited in Arabidopsis Col-0 by exposure to daily 4h HL over 5 days. Using this procedure on over-expressing (OE) and null mutant plants, it was shown that BBX32 is a negative regulator of dynamic acclimation. The same modeling connected BBX32 to the TR gene LONG HYPOCOTYL5 (HY5), but unlike BBX32, HY5 was shown to positively regulate dynamic acclimation. The severely diminished response to daily HL of BBX32–OE/hy5 plants suggest that in wild type plants, BBX32 and HY5 exert a balanced, flexible and complete regulation of dynamic acclimation.

2018-08-03 | GSE78251 | GEO

Transformants of wheat GSK3/Shaggy-like kinase TaSK5 vs wild-type Col-0

Project description:A novel cold-inducible GSK3/Shaggy-like kinase cDNA (TaSK5) was isolated from winter wheat by a macroarray-based differential screening approach. Sequence analysis of TaSK5 revealed high similarity to Arabidopsis subgroup I GSK3/Shaggy-like kinases ASK-alpha, ASK-gamma and ASK-epsilon. Transgenic Arabidopsis plants overexpressing TaSK5 cDNA under the control of CaMV 35S promoter showed enhanced tolerance to salt and drought stresses. In contrast, the tolerance of the transgenic plants to freezing stress was not altered. To identify genes which are differentially regulated in the 35S:TaSK5 over-expressing Arabidopsis plants under non-stress conditions, we compared the genome-wide expression profiles of Col-0 and plants over-expressing TaSK5 using DNA microarrays. Sixty seven genes were found to be expressed at least 2-fold more strongly in 35S:TaSK5 plants than in Col-0, and 17 genes were found to be expressed at least 2-fold more strongly in Col-0 than in 35S:TaSK5 plants. Most of the TaSK5 up-regulated genes were also induced by abiotic stresses, including cold, salt and drought. These results support the involvement of TaSK5 in abiotic stress signal transduction. Keywords: transgenic vs wt Col.-0 comparison

2014-11-02 | GSE59556 | GEO

RNA-seq analysis of Arabidopsis plants overexpressing Sclerotinia sclerotiorum effector SsE1-GFP

Project description:Ten-day old seedlings of Arabidopsis wildtype Col-0, and SsE1-overexpressing lines SsE1-GFP-5 and SsE1-GFP-8 were collected for total RNA extraction. Three biological replicates were prepared for each genotype.

2021-01-25 | GSE165401 | GEO

SUMO conjugation to the pattern recognition receptor FLS2 triggers intracellular signalling in plant innate immunity

Project description:Arabidopsis lines expressing 35S::Strep-SUMO1H89R in Col-0 background were generated since the H89R SUMO1 variant simplifies MS/MS detection of SUMO conjugated lysines after trypsinization (Miller et al., 2010). Transgenic seedlings were treated with water or 250nM flg22 for 30 minutes and total protein extracts including membrane fractions were affinity purified with Pierce™ Streptavidin Magnetic Beads. LC-MS analysis of eluting proteins allowed identification of candidate SUMO-conjugated proteins in response to flg22 treatment.

2019-11-12 | PXD011552 | Pride

Gene expression profiling in Col-0 and ein2-5 seedlings under glucose depletion and glucose recovery conditions

Project description:We aimed to compare the differences in gene expression in Col-0 and ein2-5 seedlings under glucose depletion and glucose recovery conditions. Col-0 and ein2-5 seedlings were germinated in liquid 1/2 MS medium without glucose for 4 days and were then treated with or without glucose for 2 hours. mRNA seq was performed to make the comparisons.

2020-12-29 | GSE114505 | GEO

Gene expression profiling of 35S:AtMYB102-SRDXplant under salt stress treatment

Project description:Transcriptional profiling of Arabidopsis transgenic 35S:AtMYB102-SRDX plant under MS medium containing 200mM NaCl for 24h. Transgenic Arabidopsis (background : Col-0) overexpressing AtMYB102 fused to an active transcriptional repression domain (SRDX) showed strong salt tolerance.

2010-01-21 | GSE19893 | GEO

Microarray designed to find PIN polarity regulators downstream of TIR1/AFB

Project description:Roots of 5-day-old 35S::WRKY23-GR were treated for 6 hours with 10 μM DEX or DMSO, respectively. Wt Col-0 and 35S::WRKY23-SRDX plants were treated with 10 μM NAA or DMSO for 6 hours. Roots were subsequently collected for RNA isolation. All replicates were sampled in three independent experiments. Total RNA (200 μg per array) was hybridized to ATH1 Affymetrix Arabidopsis arrays in accordance with the standard procedures at the VIB Nucleomics Core. Data files containing probe level intensities (.cel files) were used for background correction and normalization was done in R (http://www.r-project.org) using the Bioconductor package affylmGUI (http://bioinf.wehi.edu.au/affylmGUI/) using the log2 scale RMA procedure. Genes with the same or contrasting WRKY23 expression profiles were selected by Pavlidis template matching in TMeV 4.0 (TIGR) (28). Finally, genes with a significant p value (< 0.001), denoting expression above background with minimum 2-fold change compared to the respective control, were retained for further analysis. First, by comparing 35S::WRKY23-GR roots with and without induction by dexamethasone, we obtained a set of 110 genes as potential WRKY23 targets, which were up-regulated in dexamethasone-treated seedlings. Next, we identified 950 genes, which were auxin-inducible in Col-0 wild type (Wt), but lost this auxin responsiveness in dominant-negative 35S::WRKY23-SRDX roots. The overlap between the two datasets yielded a list of 61 genes (Fig. S1B). Because WRKY23 acts downstream of the SLR/IAA14 transcriptional repressor, this genelist was compared with previously published microarray data on auxin-treated solitary root1 (slr-1) mutant seedlings

2020-09-07 | E-MTAB-9563 | biostudies-arrayexpress

Identification of NLP2 in vivo targets using ChIP-Seq in Arabidopsis thaliana

Project description:Chromatin immunoprecipitation was performed in nlp2-2 Arabidopsis thaliana Col-0 14-d-old seedlings complemented by a pNLP2::NLP2-GFP construct upon 30 minutes NO3- resupply after a 3-day NO3- starvation.

2023-02-08 | GSE197357 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data