title: Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor.
abstract: Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.
authors.affiliation: Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands muino@molgen.mpg.de kerstin.kaufmann@uni-potsdam.de.
authors.forename: Jose M
authors.initials: JM
authors.lastname: Muiño
authors.affiliation: Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Suzanne
authors.initials: S
authors.lastname: de Bruijn
authors.affiliation: Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Alice
authors.initials: A
authors.lastname: Pajoro
authors.affiliation: Laboratory of Molecular Plant Biology, Department of Biology, University of Leuven (KU Leuven), Leuven, Belgium.
authors.forename: Koen
authors.initials: K
authors.lastname: Geuten
authors.affiliation: Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
authors.affiliation: Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands Bioscience, Plant Research International, Wageningen, The Netherlands.
authors.forename: Gerco C
authors.initials: GC
authors.lastname: Angenent
authors.affiliation: Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany muino@molgen.mpg.de kerstin.kaufmann@uni-potsdam.de.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Kaufmann
mesh_terms: D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics*; D047369:Chromatin Immunoprecipitation; D017124:Conserved Sequence; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000235:genetics*; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D018398:Homeodomain Proteins; C121158:SEP3 protein, Arabidopsis; D014157:Transcription Factors
keywords: MADS-domain transcription factor; cis-regulatory evolution; plant development