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Series GSE14635 Query DataSets for GSE14635
Status Public on Apr 21, 2009
Title Target genes of the MADS transcription factor SEPALLATA3, ChIP-chip
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by array
Summary The molecular mechanisms by which floral homeotic genes act as major developmental switches to specify the identity of floral organs, are still largely unknown. Floral homeotic genes encode transcription factors of the MADS-box family, which are supposed to assemble in a combinatorial fashion into organ-specific multimeric protein complexes. Major mediators of protein interactions are MADS-domain proteins of the SEPALLATA subfamily, which play a crucial role in the development of all types of floral organs. In order to characterize the roles of the SEPALLATA3 transcription factor complexes at the molecular level, we analyzed genome-wide the direct targets of SEPALLATA3. We used chromatin immunoprecipitation followed by ultrahigh-throughput sequencing or hybridization to whole-genome tiling arrays to obtain genome-wide DNA-binding patterns of SEPALLATA3. The results demonstrate that SEPALLATA3 binds to thousands of sites in the genome. Most potential target sites that were strongly bound in wild-type inflorescences, are also bound in the floral homeotic agamous mutant, which displays only the perianth organs, sepals and petals. Characterization of the target genes shows that SEPALLATA3 integrates and modulates different growth-related and hormonal pathways in a combinatorial fashion with other MADS-box proteins and possibly with non-MADS transcription factors. In particular, the results suggest multiple links between SEPALLATA3 and auxin signaling pathways. Our gene expression analyses link the genomic binding site data with the phenotype of plants expressing a dominant repressor version of SEPALLATA3, suggesting that it modulates auxin response to facilitate floral organ outgrowth and morphogenesis. Furthermore, the binding of the SEPALLATA3 protein to cis-regulatory elements of other MADS-box genes and expression analyses reveal that this protein is a key component in the regulatory transcriptional network underlying the formation of floral organs.

Keywords: ChIP-chip
 
Overall design ChIP experiments were performed on Arabidopsis wildtype inflorescences using an antibody raised against a C-terminal peptide of SEP3. For the control experiment, we used unamplified, sheared chromatin from the same biological sample like the ChIP-DNA (“input DNA”).
 
Contributor(s) Kaufmann K, Muino JM, Jauregui R, Airoldi C, Smaczniak C, Krajewski P, Angenent G
Citation(s) 19385720
Submission date Jan 29, 2009
Last update date May 09, 2017
Contact name Gerco Angenent
E-mail gerco.angenent@wur.nl
Organization name Plant Research International
Street address Bornsesteeg 65
City Wageningen
ZIP/Postal code 6708 PD
Country Netherlands
 
Platforms (1)
GPL10977 [At35b_MR] Affymetrix Arabidopsis Tiling 1.0R Array
Samples (4)
GSM365390 SEP3_replicate 1_ChIP_sample
GSM365391 SEP3_replicate 1_Input
GSM365392 SEP3_replicate 2_ChIP_sample
This SubSeries is part of SuperSeries:
GSE14636 Target genes of the MADS transcription factor SEPALLATA3
Relations
BioProject PRJNA114431

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE14635_RAW.tar 159.0 Mb (http)(custom) TAR (of BAR, CEL)
Processed data provided as supplementary file
Raw data provided as supplementary file

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