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Series GSE21301 Query DataSets for GSE21301
Status Public on Apr 13, 2010
Title Orchestration of development by the bifunctional transcription factor, APETALA2
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The emerging picture of transcriptional regulation is one of unexpected complexity. It is now clear that single transcription factors control hundreds, if not thousands, of direct targets by binding their genomic loci, but it is not understood how many of these are major players and how many are supporting cast. To address this, we leverage a well-characterized developmental network in Arabidopsis and map genome-wide binding of related proteins in multiple tissues. The transcription factor APETALA2 (AP2) has numerous functions, including roles in floral organ identity, seed development and stem cell maintenance. We focus on the role of AP2 in the floral transition and map direct targets on a genome-wide scale. We show that ap2 mutants flower early in long and short days, and that AP2 binds to many loci, most prominently floral pathway integrators, microRNAs and floral organ identity genes, many of which exhibit AP2-dependent transcription. Opposing, logical effects are evident in AP2 binding to two developmental microRNA genes that control AP2 expression, with AP2 positively regulating miR156 and negatively regulating miR172, forming a complex direct feedback loop, which also included all but one of the AP2-like miR172 target clade members. We also seek conserved targets by comparing the genome-wide direct target repertoire of AP2 with that of SCHLAFMÜTZE (SMZ), another member of the AP2-like miR172 target clade that shares partial redundancy, as evidenced by a hexuple mutant for the entire clade that flowered extremely early. Clear similarities and divergence are exposed in the AP2 and SMZ direct target repertoires. Finally, using an inducible expression system, we demonstrate that AP2 has dual molecular roles. It functions both as a transcriptional activator and repressor, directly inducing the expression of the floral repressor AGAMOUS-LIKE 15 (AGL15), and directly repressing the transcription of floral activators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1).
Overall design ChIP-Seq of two biological replicates for ATH-AP2 and respective control samples
Contributor(s) Yant L, Mathieu J, Dinh TT, Ott F, Lanz C, Wollmann H, Chen X, Schmid M
Citation(s) 20675573
Submission date Apr 12, 2010
Last update date Sep 04, 2019
Contact name Felix Ott
Organization name Max Planck Institute for Developmental Biology
Street address Spemannstr. 35-39
City Tuebingen
ZIP/Postal code 72076
Country Germany
Platforms (1)
GPL9302 Illumina Genome Analyzer II (Arabidopsis thaliana)
Samples (4)
GSM532325 ap2_chip_rep1
GSM532326 ap2_chip_rep2
GSM532327 ap2_ctrl_rep1
SRA SRP002328
BioProject PRJNA126567

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

Supplementary file Size Download File type/resource
GSE21301_AP2_peakregions.gff.gz 60.3 Kb (ftp)(http) GFF
GSE21301_RAW.tar 1.7 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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