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| Status |
Public on Feb 03, 2017 |
| Title |
RNA-seq of abscisic acid-reponsive transcription factors |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. Analyses of the resulting 122 ChIP-seq datasets identified 326,698 TF binding events using a stringent statistical cutoff. Based on our data, a comprehensive regulatory network in Arabidopsis thaliana was constructed. We uncovered determinants of dynamic TF binding and defined a hierarchy among TFs to explain differential gene expression and pathway feedback regulation. By extrapolating regulatory characteristics observed for the canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness, and demonstrate their utility to modulate plant resilience to osmotic stress.
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| Overall design |
Seedling were germinated and grown on nylon mesh in hydroponics for 3 days in dark before ABA or mock treatment. 10 uM ABA treatment or ethanol mock treatment for 1 to 60 hours.
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| Contributor(s) |
Song L, Huang SC, Castanon R, Ecker JR |
| Citation(s) |
27811239 |
| |
| Submission date |
Apr 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
|
| Samples (28)
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| This SubSeries is part of SuperSeries: |
| GSE80568 |
ChIP-Seq and RNA-Seq of abscisic acid-reponsive transcription factors |
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| Relations |
| BioProject |
PRJNA319318 |
| SRA |
SRP073711 |
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