Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

High resolution NO3 response of Arabidopsis Roots

ABSTRACT: This work uses a time series in order to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to NO3- provision. The experimental approach has been to monitor genome response to NO3- at 3, 6, 9, 12, 15 and 20 min, using ATH1 chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by very fast (within 3 min) gene expression modulation, involving genes/functions needed to prepare plants to use/reduce NO3-. State-space modeling (a machine learning approach) has been used to successfully predict gene behavior in unlearnt conditions. 26 Samples: 2 at time 0 with no treatment; 4 at time 3, 2 with KCL and 2 with KNO3 treatment; 4 at time 6, 2 with KCL and 2 with KNO3 treatment; 4 at time 9, 2 with KCL and 2 with KNO3 treatment; 4 at time 12, 2 with KCL and 2 with KNO3 treatment; 4 at time 15, 2 with KCL and 2 with KNO3 treatment; 4 at time 20, 2 with KCL and 2 with KNO3 treatment;

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Gabriel Krouk

PROVIDER: E-GEOD-20044 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:We investigated the morphological roots decisions of Arabidopsis in a NO3- heterogeneous medium. To do so, we used the Split-Root System which is an experimental set up to assess root decisions in nutrient heterogeneous medium. Split-root plants have been subjected to three different treatments. ‘Control KNO3’ plants received KNO3 on both sides of the root system (C.NO3) and ‘Control KCl’ plants received KCl on both sides (C.KCl) as a nitrogen deprivation treatment. 'Split' plants received KNO3 on one side (Sp.NO3) and KCl on the other side (Sp.KCl) of the root system to assess the root decision-making in a heterogeneous environment. We observed that the total lateral roots length in the Sp.NO3 and C.KCl compartments is induced as compared to C.NO3 and Sp.KCl compartments. This corresponds to a root proliferation response in strategic territories to compensate the nitrogen deprivation. To decipher the molecular basis of this morphological root response on day 4 after the beginning of the split-root treatment, we used a transcriptomic approach on roots at 2hours, 8 hours and 2 days after the beginning of the treatment. From our microarrays data, we have identified a global set of 150 genes for which the expression pattern match with the lateral roots responses. Among them, we selected 8 early marker genes of the root decisions, which allowed us to show that the shoots and the NO3- itself are essential for the decision. Finally, we tested the role of the cytokinins phytohormones as a NO3--derived systemic signal in the root decision. Interestingly, we have demonstrated that the systemic cytokinins are involved into the decision of inducing maker genes expression and making lateral roots in the Sp.NO3 compartment specifically. 36 samples were analyzed. They correspond to three biological repeats of the C.NO3, Sp.NO3, Sp.KCl and C.KCl root samples (12 samples) that we have collected at 2hours, 8 hours and 2 days (12 samples x 3 time points) after the beginning of the split-root treatment. We analyzed the normalized microarrays data by using a three way ANOVA. The three factors of the ANOVA are 1) presence/absence of NO3-, 2) split/control and 3) time. The measures of the significance of each probe were done by the Q-value method (q<0.2, panova<0.001). The genes differentially expressed between the C.NO3 and Sp.NO3 samples, and the C.KCl and Sp.KCl samples were determined by the post-hoc Tukey test (p<0.05).

Project description:affy_nitrogen_medicago - affy_nitrogen_medicago - Experiment has been designed to characterize the molecular expression patterns associated to a contrasted modification of the nitrogen status of the whole plant. The systemic effects of nitrogen status modifications are investigated and compared on non nodulated plant supplied with NO3, NH4 or nodulated plants (Sinorhizobium meliloti 2011) supplied with air. The root systems were separated in two compartments of unequal sizes (split root system). Two treatments were applied on the larger compartment in order to modulate the nitrogen status of the plant: for the S treatment, roots are supplied with nutrient solution containing 10 mM NH4NO3,, whereas for the C treatment, roots are supplied with nitrogen free medium. In the case of N2 fixing plants, N limitation was obtained by replacing air by a mixture of Ar and O2 80 per cent and 20 per cent. The effects of these treatments were investigated on roots of the minor compartment supplied continuously with either NO3 1 mM, NH4 1 mM or air (N2) and on the shoots. We were also interested in the molecular expression patterns associated to the roots deprived of N.-The root system of non-nodulated (NO3- and NH4+) or nodulated (N2) plants is split into two unequal parts and each one is installed in a separate compartment. For the S treatement, the major root part is supplied with NH4NO3 10 mM whereas the minor part is supplied with either NO3- 1mM, NH4+ 1mM or N2. For the C treatement, the major root part is supplied with nitrogen-free nutrient solution whereas the minor part is supplied with either NO3- 1mM, NH4plus 1mM or N2. Each treatement is four days long. Samples of roots of six biological types (NO3S, NO3C, NH4S, NH4C, N2S and N2C) were collected. Two biological repeats per biological types have been analyzed. The effect of the S and C treatments were investigated for each N sources by comparing Affymetrix transcriptomes (NO3C vs NO3S, NH4C vs NH4S, N2C vs N2S). Keywords: treatement (nitrogen-sufficient) vs treatement (nitrogen-limited)

Project description:Background: The Arabidopsis ANR1 gene is a key regulator of root architecture (Zhang and Forde, 1998): when ANR1 is down-regulated (by antisense or co-suppression) the resulting lines are no longer able to proliferate their lateral roots in response to localised supplies of NO3- (Zhang and Forde, 1998). ANR1 encodes a root-specific member of the MADS box family of transcription factors and is thought to be a component of a signalling pathway that links an external NO3- signal to increased meristematic activity in the lateral root meristem (Zhang et al., 1999).A major goal of our present BBSRC-funded project is to learn more about this NO3- response pathway by identifying the downstream targets of ANR1. To this end we have generated a set of transgenic lines in which ANR1 is under a novel post-translational control. This was achieved by tagging ANR1 with the steroid-binding domain of the rat glucocorticoid receptor (rGR) and expressing the fusion protein under the control of the CaMV 35S promoter. Initial results with these lines confirm that the architecture of the root system is altered in a way that correlates with the presence of the steroid inducer (dexamethasone, or DEX) and the expression of the ANR1::rGR transgene. We now wish to apply transcript analysis to one of these lines (ANGR4-12) to identify the genes whose expression is up- or down-regulated by ANR1. Sablowski and Meyerowitz (1998) successfully used an analogous approach to identify a gene that is an immediate target of the AP3 MADS-box transcription factor (although here, in the absence of microarray technology, differential display was used). Experimental: Plants of the two genotypes (ANGR4-12 and wild type) will be grown in sterile liquid culture for 3-4 weeks and then starved of N for 3 d (to quench the endogenous NO3- signalling pathway) before starting the DEX treatment. Roots will be harvested after 60 min from roots of DEX-treated and mock-treated RGR4-12 and control plants (four RNA samples). To minimise background noise due to environmental variables we will repeat the experiment three times and pool the RNA samples. Keywords: strain_or_line_design

Dataset Information

High resolution NO3 response of Arabidopsis Roots

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets