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Series GSE89638 Query DataSets for GSE89638
Status Public on Jan 01, 2018
Title Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species
Organism Arabis alpina
Experiment type Expression 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 that only 17% of their BSs 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 leaves and apices mRNA profiles of 10-day old wild type (WT) and pep1-1 mutant of arabis alpina (accession pajares) were generated by deep sequencing, in triplicate
 
Contributor(s) Mateos JL
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Submission date Nov 08, 2016
Last update date May 15, 2019
Contact name Julieta L Mateos
E-mail(s) jmateos@leloir.org.ar
Organization name Fundacion Instituto Leloir
Street address Av. Patricias Argentinas 435
City Buenos Aires
ZIP/Postal code C1405BWE
Country Argentina
 
Platforms (1)
GPL22647 Illumina HiSeq 2000 (Arabis alpina)
Samples (12)
GSM2385855 WT_R1_leaf
GSM2385856 WT_R2_leaf
GSM2385857 WT_R3_leaf
Relations
BioProject PRJNA352782
SRA SRP092886

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
GSE89638_apex_raw_counts.txt.gz 768.8 Kb (ftp)(http) TXT
GSE89638_leaf_raw_counts.txt.gz 784.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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