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Series GSE24568 Query DataSets for GSE24568
Status Public on May 13, 2011
Title A biophysical DNA binding model for the LEAFY transcription factor reveals the evolutionary fluidity of its binding sites
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Despite great advances in sequencing capacity, generating functional information for non-model organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence combined with the characterization of regulatory molecules from model species. Here, we focus on the LEAFY (LFY) transcription factor, a conserved master regulator of floral development. Starting with biochemical and structural information, we built a biophysical model describing LFY DNA binding specificity in vitro that accurately predicts in vivo LFY binding sites in the Arabidopsis thaliana genome. Extending the model to other species, we show that it can correctly identify functional homologs of known LFY targets from Arabidopsis thaliana in other angiosperms, even if a functional shift between orthologs and paralogs has occurred. Moreover, this model demonstrates the evolutionary fluidity of the link between LFY and one of its target genes, underlining how this regulatory interaction can be conserved despite changes in position, sequence and affinity of the LFY binding sites. Our study shows that the cis-element fluidity recently illustrated in animals also exists in plants, and that it can be detected without any experimental work in each individual species, using a biophysical transcription factor model.
Overall design A. thaliana LEAFY ChIP-seq w control, 2 replicates
Contributor(s) Moyroud E, Minguet EG, Ott F, Yant L, Posé D, Blanchet S, Monniaux M, Bastien O, Thévenon E, Weigel D, Schmid M, Parcy F
Citation(s) 21515819
Submission date Oct 07, 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)
GSM605654 lfy-ctrl-rep1
GSM605655 lfy-ctrl-rep2
GSM605656 lfy-samp-rep1
SRA SRP003928
BioProject PRJNA132641

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE24568_RAW.tar 320.8 Mb (http)(custom) TAR (of BED)
GSE24568_README.txt.gz 554 b (ftp)(http) TXT
GSE24568_lfy-peaks.txt.gz 69.2 Kb (ftp)(http) TXT
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Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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