Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide Identification of SHR Direct Targets Using a Custom Agilent Promoter Array

ABSTRACT: SHR is a key regulator of stem cell renewal and radial patterning in the Arabidopsis root. In previous studies we showed that the SHR is a transcriptional regulator and it regulates gene transcription directly. To fully understand the SHR developmental pathway, we aim to identify its direct target at the genome scale using the ChIP-on-chip method. To this end, we have designed a promoter microarray for Arabidopsis, which contains probes that tile the intergenic regions as well as the first intron and the 3' UTR for all annotated genes including miRNA genes. Chromatin immunoprecipitation (ChIP) was performed using an anti-GFP antibody on the root of a transgenic line expressing under the SHR promoter a functional fusion protein between SHR and GFP. After labeling with Cy5 and Cy3 respectively, DNA recoverd from the ChIP and mock experiments was hybridized to the same microarray. The array was scanned using an Agilent scanner and the signal intensity for each channel was retrieved and normalized by the Agilent feature extraction software. Two bilogical replicate ChIP-on-chip experiments were performed; Each array is hybridized with both ChIP and control DNA samples, which are labeled with Cy5 and Cy3 dye respectively;

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Hongchang Cui

PROVIDER: E-GEOD-21338 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth.

Sozzani R R Cui H H Moreno-Risueno M A MA Busch W W Van Norman J M JM Vernoux T T Brady S M SM Dewitte W W Murray J A H JA Benfey P N PN

Nature 20100701 7302

The development of multicellular organisms relies on the coordinated control of cell divisions leading to proper patterning and growth. The molecular mechanisms underlying pattern formation, particularly the regulation of formative cell divisions, remain poorly understood. In Arabidopsis, formative divisions generating the root ground tissue are controlled by SHORTROOT (SHR) and SCARECROW (SCR). Here we show, using cell-type-specific transcriptional effects of SHR and SCR combined with data from ...[more]

PMID: 20596025

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Project description:For potato crops, host resistance is currently the most effective and sustainable tool to manage potato root and tuber diseases caused by the plasmodiophorid, Spongospora subterranea. Arguably, zoospore root attachment is the most critical phase of the pathogen infection, however, the mechanisms underlying zoospore root attachment remains unknown. This study investigated the potential role of root cell wall surface polysaccharides and proteins in zoospore root attachment in resistant and susceptible potato cultivars. We first compared the effects of enzymatic removal of root cell wall proteins, N-linked glycans or polysaccharides on S. subterranea attachment to root tissue of resistant and susceptible potato cultivars. Subsequently, mass spectrometry analysis of peptides released by trypsin shaving (TS) of root segments identified 1235 proteins, of which 262 were differentially abundant between the resistant and susceptible cultivars. In particular, proteins associated with glutathione metabolism and lignin biosynthesis were more abundant in the resistant cultivar. Comparison with whole-root proteomic analysis of the same resistant and susceptible cultivars led to identification of 226 proteins unique to the TS dataset, of which 188 were significantly different between cultivars. Among these, the pathogen defence-related cell wall protein stem 28 kDa glycoprotein and two major latex proteins were significantly less abundant in the resistant cultivar compared to the susceptible cultivar. A further major latex protein was detected at reduced levels in the resistant cultivar in both TS and whole-root proteomic datasets. In contrast, in the TS-specific dataset, three glutathione S-transferase proteins were more abundant in the resistant cultivar, while the protein glucan endo-1,3-beta-glucosidase was significantly increased in both the TS and whole-root datasets. These results imply a particular role of major latex proteins and glucan endo-1,3-beta-glucosidase in the regulation of host susceptibility to S. subterranea.

Project description:Bacillus thuringiensis, a well-known and effective bio-insecticide, has attracted considerable attention as a potential biological control agent for the suppression of plant diseases. Treatment of tomato roots with a filter-sterilized cell-free filtrate (CF) of B. thuringiensis systemically suppresses bacterial wilt caused by Ralstonia solanacearum through systemic activation of the plant defense system. Comparative analysis of the expression of the Pathogenesis-Related 1(P6) [PR-1(P6)] gene, a marker for induced resistance to pathogens, in various tissues of tomato plants treated with CF on their roots suggested that the B. thuringiensis-induced defense system was activated in the leaf, stem, and main root tissues, but not in the lateral root tissue. At the same time, the growth of R. solanacearum was significantly suppressed in the CF-treated main root tissue but not in the CF-treated lateral root tissue. This distinct activation of the defense reaction and suppression of R. solanacearum were reflected by the differences in the transcriptional profiles of the main and lateral tissues in response to the CF. In the CF-treated main root tissue, but not CF-treated lateral root tissue, the expression of several salicylic acid (SA)-responsive defense-related genes was specifically induced, whereas jasmonic acid (JA)-related gene expression was either down-regulated or not induced in response to the CF. On the other hand, genes encoding ethylene (ET)-related proteins were induced equally in both the main and lateral root tissues. Taken together, the co-activation of SA-dependent signaling pathway with ET-dependent signaling pathway and suppression of JA-dependent signaling pathway may play key roles in B. thuringiensis-induced resistance to R. solanacearum in tomato plants. Gene expression was measured in main and lateral root tissues of tomato treated with Bacillus thuringiensis or distilled water-treated control at 48 hours after treatment. Two independent experiments were performed at each tissue (main root or lateral root tissue) for each treatment (Bacillus thuringiensis or distilled water control).

Dataset Information

Genome-wide Identification of SHR Direct Targets Using a Custom Agilent Promoter Array

Publications

Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth.

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