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Series GSE46894 Query DataSets for GSE46894
Status Public on Feb 03, 2014
Title Developmental dynamics of DNA accessibility during flower development [DNaseI-Seq]
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programmes. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Here, we characterize the dynamic relationship of chromatin accessibility, gene expression and DNA-binding of two MADS-domain proteins during Arabidopsis flower development. The developmental dynamics of DNA-binding of APETALA1 and SEPALLATA3 is largely independent of chromatin accessibility, and our findings suggest that AP1 acts as ‘pioneer factor’ that modulates chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Our data provide a primer to the idea that cellular differentiation in plants can be associated to dynamic changes in chromatin accessibility, as consequence of the action of master transcription factors.
 
Overall design We used the AP1-GR system to conduct DNaseI hypersensitivity experiments at different stages of flower development. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect before treatment and 2, 4 and 8 days after treatment. As control, naked DNA from wild-type inflorescences was used. Experiments were done in two biological replicates.
The GSE47981 includes expression data that are complementary to the data in the GSE46986 and GSE46894.
 
Contributor(s) Pajoro A, Madrigal P, Kaufmann K
Citation(s) 24581456
Submission date May 14, 2013
Last update date May 15, 2019
Contact name Alice Pajoro
E-mail(s) alice.pajoro@wur.nl
Organization name Wageningen University
Street address Droevendaalsesteeg 1
City Wageningen
ZIP/Postal code 6708lt
Country Netherlands
 
Platforms (1)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
Samples (5)
GSM1139912 DNaseI-seq 0d biological reps 1 and 2
GSM1139913 DNaseI-seq 2d biological reps 1 and 2
GSM1139914 DNaseI-seq 4d biological reps 1 and 2
This SubSeries is part of SuperSeries:
GSE46987 Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
Relations
BioProject PRJNA202977
SRA SRP022587

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
GSE46894_RAW.tar 790.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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