DNA-binding specificities of plant transcription factors and their potential to define target genes

Abstract

Significance We described the high-throughput identification of DNA-binding specificities of 63 plant transcription factors (TFs) and their relevance as cis- regulatory elements in vivo. Almost half of the TFs recognized secondary motifs partially or completely differing from their corresponding primary ones. Analysis of coregulated genes, transcriptomic data, and chromatin hypersensitive regions revealed the biological relevance of more than 80% of the binding sites identified. Our combined analysis allows the prediction of the function of a particular TF as activator or repressor through a particular DNA sequence. The data support the correlation between cis- regulatory elements in vivo and the sequence determined in vitro. Moreover, it provides a framework to explore regulatory networks in plants and contributes to decipher the transcriptional regulatory code.