Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor

J.M. Muiño*, S.A. de Bruijn, A. Pajoro, Koen Geuten, Martin Vingron, G.C. Angenent, K. Kaufmann*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

27 Citations (Scopus)


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 (BS) among plant species has not yet been experimentally determined.

Here, we performed comparative ChIP-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: A. thaliana and A. lyrata which have very similar floral organ morphology. We found that binding site 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.
Original languageEnglish
Pages (from-to)185-200
JournalMolecular Biology and Evolution
Issue number1
Publication statusPublished - 2016


  • Cis-regulatory evolution
  • Mads-domain transcription factor
  • Plant development


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