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Series GSE89889 Query DataSets for GSE89889
Status Public on Jan 01, 2018
Title Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.
Organisms Arabidopsis thaliana; Arabis alpina
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found the BSs that were conserved in both species, and that these contained a CArG-box that is recognised by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared to the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated genes (COR) were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared to wild-type and this correlated with reduced growth in pep1-1. Therefore FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.
Overall design Investigation of FLC and FLC ortholog PEP1 in Arabidopsis thaliana and Arabis alpina.
Contributor(s) Mateos J, Tilmes V, Madrigal P, Coupland G
Citation(s) 29203652
Submission date Nov 15, 2016
Last update date May 15, 2019
Contact name Julieta Mateos
Phone +054 11 5238-7500
Organization name Max Planck Institute for Plant Breeding Research
Department Department of Plant Developmental Biology
Lab Control of Flowering Time
Street address Carl-von-Linné-Weg 10
City Cologne
ZIP/Postal code D-50829
Country Germany
Platforms (2)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL23515 Illumina HiSeq 2500 (Arabis alpina)
Samples (10)
GSM2392630 FLC ChIP-Seq WT rep1
GSM2392631 FLC ChIP-Seq control rep1
GSM2392632 FLC ChIP-Seq WT rep2
BioProject PRJNA353651
SRA SRP093390

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
GSE89889_FLC_peaks.csv.gz 3.2 Kb (ftp)(http) CSV
GSE89889_PEP1_peaks_new.csv.gz 2.4 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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