Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. However, until now, the evolutionary turnover and dynamics of TF binding sites among plant species has not yet experimentally determined. Here, we performed comparative ChIP-seq studies of the MADS-box TF SEPALLATA3 (SEP3) in inflorescences of two Arabidopsis species: A. thaliana and A. lyrata. Comparative RNA-seq analysis shows that the loss/gain of BSs is often followed by a change in gene expression.
Chromatin was crosslinked and isolated from wildtype A. lyrata inflorescences up to floral stage 10/11. The immunoprecipitation of protein-DNA complexes was performed using a peptide SEP3 antibody that was raised against A. thaliana SEP3, and is also able to recognize the homolog from A. lyrata due to protein similarity. As a control, de-crosslinked 'input-DNA' was used. SEP3 ChIP-seq on Arabidopsis thaliana can be found in the accessions GSM364939 and GSM364941. Re-analyzed peak positions for these samples are included as a supplementary file on the series level (SEP3Ratiobg5@TAIR10-win.csv).