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Vascular specific H3K27me3 and H3K4me3 profile in the Arabidopsis root

ABSTRACT: We isolated Vascular specific root protoplast using the pWOL:GFP marker line (Birnbaum et al., 2003) and Fluorescence Activated Cell Sorting (FACS). FACS-treated root protoplast from wild type plants (Col0) were used as control. The GFP positive protoplast from the pWOL:GFP line and WT protoplast were used for a ChIP-seq experiment using H3K27me3 and H3K4me3 antibodies.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE86429 | GEO | 2016/09/06

SECONDARY ACCESSION(S): PRJNA341847

REPOSITORIES: GEO

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Project description: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.

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Vascular specific H3K27me3 and H3K4me3 profile in the Arabidopsis root

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