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Series GSE3399 Query DataSets for GSE3399
Status Public on Sep 22, 2008
Title Identification of BABY BOOM downstream targets
Organism Arabidopsis thaliana
Experiment type Expression profiling by array
Summary A glucocorticoid-regulated BBM protein (35S:BBM-GR) was used in combination with microarray analysis to identify genes directly activated by BBM. We employed the system described by (Lloyd et al., 1994) in which dexamethasone (DEX) and cycloheximide (CHX) are applied together to respectively, induce nuclear localization of the BBM-GR protein and prevent translation of the primary targets mRNAs. In this way it is possible to identify direct targets of a transcriptional activator by comparing gene expression profiles between DEX+CHX-treated transgenic and wild-type tissues.
The ability of the 35S:BBM GR construct to induce somatic embryogenesis in Arabidopsis seedlings was determined by phenotypic observation of 35S:BBM GR seeds germinated and grown in the presence of 10 µM dexamethasone (DEX). As in 35S:BBM seedlings, we observed somatic embryo formation on the cotyledons, first leaves and shoot meristem of DEX-treated 35S:BBM GR seedlings. We identified a set of 20 genes (including BBM itself) and our analysis indicates that BBM directly activates a signaling pathway comprising transcription factors and other signaling molecules, but which does not initially include genes known to induce somatic embryogenesis, such as LEC1, LEC2 or WUS. The functions of the BBM target genes are unknown, however a number of them have recently been identified in microarray screens for meristem-expressed genes. The identification of BBM-interacting partners and downstream targets provides new tools for unraveling pathways related to plant cell growth and organogenesis.
Keywords: transcriptional activation
Overall design To identify candidate BBM targets, we treated 4 day old 35S:BBM-GR seedlings for 8 hours with 10 µM DEX in the presence of 10 µM CHX and compared the mRNA population from these seedlings using Arabidopsis Operon microarrays ( to that of 4 day old wild-type seedlings treated in the same way. The seed batches used in this analysis showed 100% EFS when grown continuously on media with 10 µM DEX. Four day old seedlings were chosen as the experimental material because they are highly responsive to BBM GR activation and provide sufficient RNA for the microarray experiments. The biological reproducibility of the data was monitored using two independent single locus 35S:BBM GR lines. The technical reproducibility of the data was monitored using two independently DEX + CHX-treated samples from each transgenic line. Dye effects were monitored in a dye-swap experiment using one of the four RNA samples from the two biological replicates
Contributor(s) Passarinho P, Fukuoka H, Xing M, van Arkel J, Immink R, Joosen R, Maliepaard C, Lammers M, Herdies L, den Boer B, van der Geest L, Boutilier K
Citation(s) 18663586
Submission date Sep 30, 2005
Last update date Mar 16, 2012
Contact name Paul Passarinho
Organization name Plant Research International BV
Department Business Unit Bioscience
Lab Plant developmental systems
Street address Bornsesteeg 65
City Wageningen
ZIP/Postal code 6708 PD
Country Netherlands
Platforms (1)
GPL2907 Qiagen-Operon Arabidopsis 28.8k Genome Array (AtOligo 1.16.2.Y)
Samples (10)
GSM76477 Array 1-16-15 (WT DC vs. GR#1A DC)
GSM76479 Array 1-16-16 (WT DC vs. GR#1B DC)
GSM76480 Array 1-16-17 (GR#1A DC vs. WT DC)
BioProject PRJNA93529

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