Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Arabidopsis FACS sorted root specific cell types after nitrogen treatment

ABSTRACT: The organs of multicellular species are comprised of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change but little is known about how responses are tailored to specific cell types or coordinated among them on a global level. Here we use cellular profiling of five Arabidopsis root cell types in response to a limiting resource, nitrogen, to uncover a vast and predominantly cell-specific response that was largely undetectable using traditional methods. These methods reveal a new class of cell-specific nitrogen responses. As a proof-of-principle, we dissected one cell-specific response circuit that mediates nitrogen-induced changes in root branching from pericycle cells. Thus, cellular response profiling links gene modules to discrete functions in specific cell types. Experiment Overall Design: The whole experiment was carried out in triplicate with 84 chips in total (28 experiments). The nitrogen response in 5 FACS-sorted root cell types (LRC, lateral root cap; EpiC, epidermis and cortex; EndoP, endodermis and pericycle; Peri, pericycle; Stele, stele), protoplasts and Col-0 whole roots was assayed using microarrays. 5mM KNO3 was used as a nitrogen treatment for 2 hours. 5mM KCl was used as a control treatment for the same length of time. 1mM MSX in combination with 5mM KNO3 (or with 5mM KCl as a control) was used to block the assimilation of KNO3, and 5mM Gln added to restore it in order to separate KNO3 effects from assimilated-nitrogen effects. 5mM KNO3 was either maintained in the protoplast-generating solution (continuous treat) or not (transitory treat) to test how to best preserve the cellular nitrogen-response during the 1 hr protoplast generating procedure. As controls we used protoplasts, whole roots frozen directly after the 2hr treatment or 3.5hr treatment, or whole roots incubated in protoplast-generating solution (minus enzymes; transitory or continuous treated) and then frozen. After FACS-sorting or mock FACS-sorting cells were frozen.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Kenneth David Birnbaum

PROVIDER: E-GEOD-7631 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cell-specific nitrogen responses mediate developmental plasticity.

Gifford Miriam L ML Dean Alexis A Gutierrez Rodrigo A RA Coruzzi Gloria M GM Birnbaum Kenneth D KD

Proceedings of the National Academy of Sciences of the United States of America 20080107 2

The organs of multicellular species consist of cell types that must function together to perform specific tasks. One critical organ function is responding to internal or external change. Some cell-specific responses to changes in environmental conditions are known, but the scale of cell-specific responses within an entire organ as it perceives an environmental flux has not been well characterized in plants or any other multicellular organism. Here, we use cellular profiling of five Arabidopsis r ...[more]

PMID: 18180456

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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).

Dataset Information

Transcription profiling of Arabidopsis FACS sorted root specific cell types after nitrogen treatment

Publications

Cell-specific nitrogen responses mediate developmental plasticity.

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