Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of Arabidopsis shoots and roots whose nitrate levels and IPT3 expression are manipulated in a shoot-specific manner

ABSTRACT: In plants, nitrate is suggested to act as an indicator of nitrogen (N) status that modulates N responses under steady-state conditions. Our preceding study suggested that shoot nitrate accumulation alone represses expression of N starvation-inducible genes in shoots and roots. Notably, we observed that shoot nitrate accumulation was accompanied by increases in shoot expression of ISOPENTENYL TRANSFERASE 3 (IPT3) and shoot levels of N6-(Δ2-isopentenyl) adenine (iP)-type CK. IPT3 expression is localized primarily in phloem companion cells, and iP-type CKs, which are synthesized by IPT3, are phloem-mobile. Hence, both local and systemic responses to shoot nitrate status may be regulated by IPT3-synthesized iP-type CKs. Thus, the present study aims to dissect the local/systemic responses to shoot nitrate status and their dependence on shoot IPT3. To achieve this, we developed a novel experimental system to manipulate nitrate levels and IPT3 expression in a shoot-specific manner using grafted plants derived from the plants lacking nitrate reductase and/or IPT3. Using shoots and roots from the grafted plants, RNA-seq analysis was performed.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Takushi HACHIYA

PROVIDER: E-MTAB-14302 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of the shoots of Arabidopsis wild-type and mutants deficient in either or both activities of nitrate reductase and alternative oxidase

Project description:The conversion of nitrate to ammonium, known as nitrate reduction, consumes large amounts of reductants in plants. Previous studies have observed that mitochondrial alternative oxidase (AOX) is upregulated under conditions of limited nitrate reduction, such as low or no nitrate availability, or when ammonium serves as the sole nitrogen (N) source. Electron transfer from ubiquinone to AOX bypasses the proton-pumping complexes III and IV, thereby consuming reductants efficiently. Therefore, the upregulation of AOX under conditions of limited nitrate reduction may help dissipate excessive reductants and mitigate oxidative stress. However, firm evidence supporting this hypothesis is lacking due to the absence of experimental systems capable of directly analyzing the relationship between nitrate reduction and AOX. To address this gap, we developed a novel culturing system that allows for the manipulation of nitrate reduction and AOX activities separately, without inducing N starvation, ammonium toxicity, or disrupting the nitrate signal. Using this system, we investigated genome-wide gene expression with RNA-seq to gain insight into the relationship between AOX and nitrate reduction.

2024-04-23 | E-MTAB-14027 | biostudies-arrayexpress

Transcriptome analysis of the shoots of Arabidopsis wild-type and ammonium-insensitive mutant plants grown under 10 mM ammonium as sole nitrogen source

Project description:Abundant ammonium nutrition impairs plant growth, i.e. ammonium toxicity, the primary cause of which remains to be determined. To obtain a clue about the toxic mechanism, we performed microarray experiments and compared the expression of genes responsive to toxic levels of ammonium between the wild-type (Col) and an ammonium-insensitive mutant (ami2) shoots growing in media containing 10 mM ammonium.

2021-07-24 | E-MTAB-10796 | biostudies-arrayexpress

Transcriptome analysis of Arabidopsis wild-type and NRT1.1-knockout mutant seedlings grown under 10 mM ammonium as sole nitrogen source

Project description:High levels of ammonium as the sole nitrogen source impairs plant growth, i.e. ammonium toxicity, the primary cause of which remains to be determined. To obtain a clue about the toxic mechanism, we compared genome-wide gene expression between the wild-type (Col) and NRT1.1-knockout mutant (chl1-5, nrt1.1) seedlings growing in media containing toxic levels of ammonium as the sole nitrogen source.

2023-10-31 | E-MTAB-13395 | biostudies-arrayexpress

Response of grapevine shoot apex expression to grafting with rootstocks

Project description:The transcriptional response in the shoot apex to hetero-grafting Cabernet Sauvignon (CS) with the rootstocks 1103 Paulsen (CS/1103P) and Riparia Gloire de Montpellier (CS/RG) compared to the auto-grafted control (CS/CS) four months after grafting. Gene expression profiling was done using the Nimblegen whole genome array with 4 biological replicates of 5 pooled shoot apices.

2014-01-11 | E-MTAB-1523 | biostudies-arrayexpress

Effects of root-specific activation of plasma membrane H+-ATPase 1 on genome-wide gene expression in A. thaliana roots

Project description:Plasma membrane (PM) H+-ATPase contributes to nutrient uptake and stomatal opening by creating proton gradient across the membrane. A dominant mutation in the OPEN STOMATA2 locus (OST2-2D) constitutively activates Arabidopsis PM H+-ATPase 1 (AHA1), enlarging proton motive force for root nutrient uptake. However, the stomatal opening is also constitutively enhanced in the ost2-2D, which results in drought hypersensitivity. Therefore, we postulated that the root-specific activation of OST2/AHA1 could be an ideal design for improving nutrient uptake efficiency without causing drought hypersensitivity. Accordingly, we grafted Col-0 (WT) scions onto rootstock originating from WT or ost2-2D and analyzed the vegetative growth, nutrient element content, and transcriptomes of the grafted plants grown under nutrient-rich or -poor conditions.

2022-06-22 | E-MTAB-11843 | biostudies-arrayexpress

Enhanced photorespiratory and TCA pathways by elevated CO2 to manage ammonium nutrition in tomato leaves

Project description:This work aims to study wether the increment of the atmospheric carbon dioxide (CO2) concentration, in the context of climate change, will potentially allow plants to better face ammonium nutrition. Tomato (Solanum lycopersicum L.) plants were grown for 4 week with 15 mM of nitrogen, supplied as nitrate or ammonium, in conditions of ambient (aCO2, 400 ppm) or elevated CO2 (eCO2, 800 ppm) atmosphere. Transcription profiling by array was carried out in leavesfor the four growth conditions assayed and gene expression comparisons were done between N sources and CO2 conditions: i) genes differentially expressed in response to the atmospheric CO2 concentration (eCO2 vs aCO2) under nitrate or ammonium nutrition; ii) genes differentially expressed in response to the N source (ammonium vs nitrate) at aCO2 or eCO2. 3 biological replicates for each growth condition were analysed.

2024-11-29 | E-MTAB-14587 | biostudies-arrayexpress

Transcription profiling by array of Vitis rootstock roots to investigate the effects of N supply on different rootstock/scion genotype combinations

Project description:Because nitrogen (N) nutrition is a key determinant of plant growth, we explored the role of N availability in grafted grapevine development. Vitis vinifera cv. Cabernet Sauvignon was grafted on two rootstock genotypes known to confer high (1103 Paulsen, 1103P) and low (Riparia Gloire de Montpellier, RGM) vigour. One-year-old plants were cultivated in sand-filled pots in a greenhouse and irrigated with the control nutrient solution for 15 days of acclimation (1.6 mM N). At the end of the acclimation period (0 days post treatment (dpt)), the plants were divided in two groups of 5 plants per combination and irrigated with nutrient solutions varying only in their nitrate concentration (0.8 mM (Nitrate -) and 2.45 mM (Nitrate +)). Roots were harvested at 15 and 60 dpt. Gene expression profiling was done using the Nimblegen whole genome array with 3 biological replicates per condition to analyze the combined effect of N treatment and rootstock genotype on gene expression.

2016-04-01 | E-MTAB-3062 | biostudies-arrayexpress

Transcription profiling of Arabidopis nai1-1, ER body deficient mutant, vs wild-type Col-0

Project description:ER bodies are endoplasmic reticulum (ER)-derived organelles that might be involved in defense systems. The NAI1 gene regulates the development of ER bodies because mutation of NAI1 abolishes the formation of ER bodies. The nai1-1 mutant had a single nucleotide change at an intron acceptor site of At2g22770 (NAI1 gene). Because of this mutation, aberrant splicing of NAI1 mRNA occurs in the nai1-1 mutant. NAI1 encodes a transcription factor that has a basic-helix-loop-helix (bHLH) domain. Transient expression of NAI1 induced ER bodies in the nai1-1 mutant. To identify genes that are related to ER bodies, we compared the genome-wide expression profiles of Col-0 and the nai1-1 mutant using DNA microarrays. Twenty-nine genes were found to be expressed at least 2-fold more strongly in the nai1-1 mutant than in Col-0, and 341 genes were found to be expressed at least 2-fold more strongly in Col-0 than in the nai1-1 mutant. The 15 genes that showed the strongest expression in Col-0 compared to the expression in nai1-1 are shown in Table 1. Five of these genes are JAL genes (JAL22, JAL23, JAL31, JAL33 and PBP1/JAL30). The mRNA level of PYK10 was reduced in nai1-1 (4.3 fold larger in Col-0 than in nai1-1). The mRNA levels of GLL genes (GLL23 and GLL25) were also reduced in nai1-1. Experiment Overall Design: Total RNA was purified from the roots of 20-day-old plants (3 plants were pooled for each genotype). Arabidopsis plants were grown under continuous light condition at 22ËC on MS medium paltes. The control plants and the nai1-1 mutant were cultivated in the same plate. This was done to avoid any difference in plant growth conditions between the mutants and the control plants.

2008-06-14 | E-GEOD-6446 | biostudies-arrayexpress

Genome-wide maps of PRR5 binding loci in Arabidopsis thaliana

Project description:PRR5 transcription factor acts in the circadian clock system. To elucidate bound genes by PRR5, Chimeric protein FLAG-PRR5-GFP, was expressed under PRR5 promoter in Col-0 (PRR5pro:FLAG-PRR5-GFP/prr5). ChIP was performed using anti-GFP antibody (ab290;Abcam), which was bound to Dynabeads Protein G (100-03D;Life technologies), and ChIP DNA and input DNA were analyzed by Illumina GA II. ChIP and input sequence reads were compared to find out PRR5 binding sites

2012-09-20 | E-GEOD-36361 | biostudies-arrayexpress

The effect of over-expression of PRR5-VP in Arabidopsis seedlings

Project description:PRR5 transcription factor acts in the circadian clock system. To elucidate regulated genes by PRR5, Chimeric protein PRR5-VP, which activates direct target genes of PRR5, was over-expressed in Col-0. Microarray analsysis was performed using these plants with Affymetrix ATH1 genechip. PRR5-VP expressing plants and its parental plants (accession Col-0, described as Wild) were grown under 12 hr light / 12 hr dark conditions, and harvested at ZT6(6 hr after light on), ZT12, and ZT18

2012-09-20 | E-GEOD-36360 | biostudies-arrayexpress

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