Transcriptomics

Dataset Information

4

Identification of BABY BOOM downstream targets


ABSTRACT: 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 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 (http://www.ag.arizona.edu/microarray/) 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

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Hiroyuki Fukuoka  Paul Passarinho  Lydia Herdies  Jeroen van Arkel  Richard Immink  Ronny Joosen  Bart den Boer  Michiel Lammers  Lonneke van der Geest  Kim Boutilier  Meiqing Xing  Chris Maliepaard 

PROVIDER: E-GEOD-3399 | ArrayExpress | 2010-06-25

SECONDARY ACCESSION(S): GSE3399PRJNA93529

REPOSITORIES: GEO, ArrayExpress

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Publications

BABY BOOM target genes provide diverse entry points into cell proliferation and cell growth pathways.

Passarinho Paul P   Ketelaar Tijs T   Xing Meiqing M   van Arkel Jeroen J   Maliepaard Chris C   Hendriks Mieke Weemen MW   Joosen Ronny R   Lammers Michiel M   Herdies Lydia L   den Boer Bart B   van der Geest Lonneke L   Boutilier Kim K  

Plant molecular biology 20080729 3


Ectopic expression of the Brassica napus BABY BOOM (BBM) AP2/ERF transcription factor is sufficient to induce spontaneous cell proliferation leading primarily to somatic embryogenesis, but also to organogenesis and callus formation. We used DNA microarray analysis in combination with a post-translationally regulated BBM:GR protein and cycloheximide to identify target genes that are directly activated by BBM expression in Arabidopsis seedlings. We show that BBM activated the expression of a large  ...[more]

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