Genomics

Dataset Information

102

Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.


ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000 (Arabidopsis thaliana)

SUBMITTER: Julieta Mateos  

PROVIDER: GSE89889 | GEO | 2018-01-01

SECONDARY ACCESSION(S): PRJNA353651

REPOSITORIES: GEO

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Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species.

Mateos Julieta L JL   Tilmes Vicky V   Madrigal Pedro P   Severing Edouard E   Richter René R   Rijkenberg Colin W M CWM   Krajewski Paweł P   Coupland George G  

Proceedings of the National Academy of Sciences of the United States of America 20171204 51


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 Ar  ...[more]

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