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| 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
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| 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 SCHLAFMĂTZE (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).
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| Overall design |
ChIP-Seq of two biological replicates for ATH-AP2 and respective control samples
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| 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
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| Street address |
Spemannstr. 35-39
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| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
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| Platforms (1) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
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| Samples (4)
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| Relations |
| SRA |
SRP002328 |
| BioProject |
PRJNA126567 |
| 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 Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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