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Series GSE46986 Query DataSets for GSE46986
Status Public on Feb 03, 2014
Title Developmental dynamics of floral gene regulation [ChIP-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 chromatin immunoprecipitation experiments with SEP3-specific antibodies and GR atibodies followed by deep-sequencing (ChIP-Seq) in order to determine SEP3 and AP1 binding sites on a genome-wide scale. 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 2, 4 and 8 days after treatment. As control, we performed ChIP experiments using pre-immune serum at the different time points. Experiments were done in two biological replicates for 4 days and 8 days time-points while one biological replicate was done for control samples and 2 days time-point.
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 15, 2013
Last update date May 15, 2019
Contact name Alice Pajoro
Organization name Wageningen University
Street address Droevendaalsesteeg 1
City Wageningen
ZIP/Postal code 6708lt
Country Netherlands
Platforms (2)
GPL9302 Illumina Genome Analyzer II (Arabidopsis thaliana)
GPL17970 Illumina MiSeq (Arabidopsis thaliana)
Samples (11)
GSM1142624 SEP3 ChIP-seq 4d biological reps 1 and 2
GSM1142625 SEP3 ChIP-seq 8d biological reps 1 and 2
GSM1142626 AP1 ChIP-seq 2d biological replicate 1
This SubSeries is part of SuperSeries:
GSE46987 Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
BioProject PRJNA203220
SRA SRP022770

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
GSE46986_AP1_2days.txt.gz 13.0 Kb (ftp)(http) TXT
GSE46986_RAW.tar 410.0 Kb (http)(custom) TAR (of TXT)
GSE46986_SEP3_2days.txt.gz 44.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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