15th International Conference on Arabidopsis Research - TAIR

T10-043
Toward the high throughput identification of the
binding sites of TGA transcription factors using a
whole-genome promoter array
Françoise Thibaud-Nissen(1), Julia Redman(1), Christopher Johnson(2), Todd
Richmond(3), Roland Green(3), Jonathan Arias(2), Christopher Town(1)
1-The Institute for Genomic Research, Rockville, MD, USA
2-Department of Biological Sciences, University of Maryland, Baltimore County, MD, USA
3-NimbleGen, Madison, WI, USA
TGA transcription factors govern the expression of genes that confer protection
against xenobiotic stress and microbial pathogens. In Arabidopsis,
TGA2 and TGA3 regulate the transcription of Pathogenesis-Related 1 (PR1)
and presumably other host-defense genes, which together contribute to the
establishment of systemic acquired resistance (SAR). However, differences in
DNA-binding properties within the 10-member Arabidopsis TGA transcription
factor family imply that they are likely to have both distinct and shared sets
of target genes. This hypothesis is supported by the diversity of expression
patterns that we observe in plants expressing TGA promoter-GUS or -GFP fusions.
Consequently, one of our goals is to identify the genome-wide binding
sites for each Arabidopsis TGA transcription factor. To this end, labeled probes
derived from chromatin, immunoprecipitated with antibodies specific to
each TGA factor are hybridized to arrays representing Arabidopsis promoter
regions (ChIP-chip). The quality of the ChIP samples obtained with anti-TGA3
and TGA2 antibodies was assessed using an array representing approximately
200 Arabidopsis promoters, and was confirmed by real-time PCR.
Moreover, in collaboration with NimbleGen we have developed an Arabidopsis
chip representing the promoter regions of the 27,100 genes in the TIGR
annotation. By hybridizing mock ChIP samples to this array, we were able to
exclusively identify promoters that had been artificially enriched. Hybridizations
of bona fide ChIP samples from salicylic acid (SA)-treated plants to this
whole-genome promoter array are in progress and results will be presented.
In parallel, we are using Affymetrix ATH1 arrays to analyze gene expression
in response to SA in wild-type and mutant plants. Collectively, the clustered
expression profiles, ChIP analysis and spatial patterns of expression will form
the foundation for developing a model for the transcriptional network of TGA
factors in Arabidopsis.
This work is supported by the National Science Foundation’s 2010 Project.
T10 Novel Tools, Techniques and Resources
T10-044
Transcriptome and proteome analysis of the light
induced greening of an Arabidopsis cell culture
Yasuo Niwa(1, 2), Anne von Zychlinski(1), Torsten Kleffmann(1), Philip
Zimmermann(1), Wilhelm Gruissem(1), Sacha Baginsky(1)
1-Institute of Plant Science, ETH Zurich, Switzerland
2-University of Shizuoka
Light regulates many different aspects of plant development and function
such as photosynthesis, photo morphogenesis, phototropism, chloroplast
development, and movement. Regulation mechanisms of light dependent
gene expression are still largely unknown. The light-induced greening of an
Arabidopsis cell culture was used to characterize light dependent changes at
mRNA and protein levels. The green cultured cells turned yellow under dark
condition and greening can be induced again upon illumination.
We used Affymetrix Genechip® technology for transcriptional profiling of
the greening process. In addition, proteome analysis was carried out using
an LC/MS/MS technology approach. While genes related to photosynthesis
were induced at the mRNA levels, we could not detect significant changes at
the protein level. The comparison of transcriptome and proteome data will be
discussed.
15 th <strong>International</strong> <strong>Conference</strong> on Arabidopsis Research 2004 · Berlin