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Salicylic acid-induced gene expression in wild-type Col-0 and mutant ube4 Arabidopsis thaliana plants

ABSTRACT: Salicylic acid-induced gene expression in wild-type Col-0 and mutant ube4 Arabidopsis thaliana plants

PROVIDER: PRJEB29533 | ENA |

REPOSITORIES: ENA

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Salicylic acid-induced gene expression in wild-type Col-0 and mutant upl3-4 Arabidopsis thaliana plants.

Project description:Activation of plant immunity is associated with dramatic transcriptome reprogramming to prioritise immune responses over normal cellular functions. Changes in gene expression are coordinated by the immune hormone salicylic acid (SA). Here we investigated the involvement of the HECT-type ligase Ubiquitin Protein Ligase 3 (UPL3) in SA-induced transcriptional reprogramming. We show that UPL3 acts as an amplifier of SA-induced changes in gene expression. Four-week old Arabidopsis thaliana plants of wild-type Col-0 and mutant upl3-4 genotypes were germinated on soil in 100% relative humidity. After 12 days plants were transplanted to larger pots (six plants per pot) and grown for an additional 3 weeks before experimental treatment. Plants were continuously grown in an environmental chamber with 16/8 hour day/night light regime (120 mol m-2 s-1 light intensity), 21/18 degrees celcius day/night cycle and 65% relative humidity. Plants were then sprayed with water or 0.5 mM SA until all leaves were thoroughly covered with fine droplets. After 24 hours leaf tissue was harvested from 6 plants per treatment and pooled together into a single biological repeat. In total two or three independent biological repeats were collected. After harvesting leaf tissue was immediately frozen in liquid nitrogen until further analysis.

2018-11-09 | E-MTAB-7374 | biostudies-arrayexpress

Salicylic acid-induced gene expression in wild-type Col-0 and mutant upl1, upl5, and npr1-1 Arabidopsis thaliana plants

Project description:The plant immune hormone salicylic acid (SA) modulates transcriptional reprogramming via controlling the master transcriptional coactivator, NPR1. Here we examined the role of HECT-type ubiquitin ligases, UPL1 and UPL5, in SA/NPR1-dependent transcriptional control. We showed that UPL1 and UPL5 are essential regulators of SA-responsive genes, and regulate SA-induced transcriptional reprogramming in a NPR1-dependent manner. Four-week old Arabidopsis thaliana plants of wild-type Col-0, mutant upl1, mutant upl5, and mutant npr1-1 genotypes were germinated on soil in 100% relative humidity. Plants were continuously grown in an environmental chamber with 16/8 hour day/night light regime (120 mol m-2 s-1 light intensity), 21/18 degrees celcius day/night cycle and 65% relative humidity. 4-week-old plants were sprayed with water or 0.5 mM SA until all leaves were thoroughly covered with fine droplets, samples were collected after 24 hours treatment. In total two independent biological repeats were collected.

2021-10-05 | E-MTAB-10963 | biostudies-arrayexpress

Transcriptome analyses of Pst DC3000-inoculated Arabidopsis thaliana Col-0 and 35S::CBP60g plants at normal and elevated temperature

Project description:We performed RNA sequencing of Pseudomonas syringae pv. tomato (Pst) DC3000-infected A. thaliana Col-0 and 35S::CBP60g plants at normal (23C) and elevated (28C) temperatures. 4-week-old plants were pre-incubated at 23C and 28C for 48h and then leaves were syringe-infiltrated with DC3000 bacterial inoculum. Plants were incubated at their respective temperatures (23C or 28C) for another 24h post-inoculation before tissue collection for RNA extraction. RNA samples for submitted for RNA sequencing and we found different clusters of DC3000-regulated genes that were similarly or differentially regulated between Col-0 and 35S::CBP60g at elevated temperature. Temperature-downregulated DC3000-induced genes in Col-0 plants that were restored in 35S::CBP60g plants were enriched for immunity/defense-related genes, including those essential for host salicylic acid (defense hormone) biosynthesis and accumulation.

2022-05-05 | GSE197771 | GEO

Salicylic acid-induced gene expression in wild-type Col-0 and mutant upl3-4 Arabidopsis thaliana plants.

Project description:Salicylic acid-induced gene expression in wild-type Col-0 and mutant upl3-4 Arabidopsis thaliana plants.

| PRJEB29530 | ENA

Salicylic acid-induced gene expression in wild-type Col-0 and mutant ube4 Arabidopsis thaliana plants

Project description:Activation of plant immunity is associated with dramatic transcriptome reprogramming to prioritise immune responses over normal cellular functions. Changes in gene expression are coordinated by the immune hormone salicylic acid (SA). Here we investigated the involvement of the E4 ubiquitin ligase UBE4/MUSE3 in SA-induced transcriptional reprogramming. We show that loss of UBE4 function results in amplified expression of SA-induced, NPR1-dependent gene expression. Twelve-day old Arabidopsis thaliana seedlings of wild-type Col-0, mutant ube4 (SAIL_713_A12) and mutant npr1-1 genotypes were grown on MS media supplemented with 1X Gamborg vitamins in an environmental chamber with 16/8 hour day/night light regime (120 mol m-2 s-1 light intensity) and 22 degrees Celcius. Seedlings were then transferred to 6-well plates and immersed in 10 ml of 0.5 mM SA or water. After 12 hours seedlings were harvested and for each treatment ~50 seedlings were pooled together into a single biological repeat. In total two independent biological repeats were collected. After harvesting seedlings were briefly dried on tissue and immediately frozen in liquid nitrogen until further analysis.

2019-03-20 | E-MTAB-7369 | biostudies-arrayexpress

Transcriptome analyses of mock- and Pst DC3000-inoculated Arabidopsis thaliana Col-0 plants at normal and elevated temperature

Project description:We performed RNA sequencing of mock-inoculated and Pseudomonas syringae pv. tomato (Pst) DC3000-infected A. thaliana (Col-0 accession) plants at normal (23C) and elevated (30C) temperatures. 4-week-old Col-0 plants were pre-incubated at 23C and 30C for 48h and then leaves were syringe-infiltrated with either mock (MgCl2) or DC3000 bacterial inoculum. Plants were incubated at their respective temperatures (23C or 30C) for another 24h post-inoculation before tissue collection for RNA extraction. RNA samples for submitted for RNA sequencing and we found different clusters of DC3000-regulated genes that were downregulated, upregulated and unchanged at elevated temperature. Temperature-downregulated DC3000-induced genes were enriched for a whole suite of defense-related genes, including those essential for host salicylic acid (defense hormone) biosynthesis and accumulation.

2022-05-05 | GSE152072 | GEO

ChIP-seq for HA-HTR5/Col-0 and Col-0 using HA antibody

Project description:To investigate the deposition of HTR5 in Arabidopsis, we analysed genome-wide HTR5 density in the wild-type Col-0 by ChIP-seq. We then performed HTR5 occupancy analysis using data obtained from ChIP-seq of 3 different plants including HA-HTR5/Col-0 and Col-0. Col-0 acted as negative control.

2023-04-01 | GSE223308 | GEO

Arabidopsis gene expression profile : Col-0 wild-type vs. pif3pif4pil5pil6 (pifQ) mutant

Project description:Transcriptional profiling of 60h-old Arabidopsis whole seedlings comparing control Col-0 wild-type plants with pifQ mutant plants The expression profile of dark-grown pifQ mutant shows similar pattern of Rc-grown Col-0 wild-type Keywords: Genetic modification

2009-04-23 | GSE14492 | GEO

Bisulfite (methylome) sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0; msh1 mutant; dcl2,3,4,msh1 quadruple mutant in Arabidopsis [msh1_graft_BS-seq]

Project description:Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the bisulfite sequencing (methylome). Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the bisulfite sequencing.

2020-09-20 | GSE152564 | GEO

Salicylic acid-induced gene expression in wild-type Col-0 and mutant upl1, upl5, and npr1-1 Arabidopsis thaliana plants

Project description:Salicylic acid-induced gene expression in wild-type Col-0 and mutant upl1, upl5, and npr1-1 Arabidopsis thaliana plants

| PRJEB47659 | ENA