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

Abstract

Transcription factors (TFs) regulate gene expression through binding to cis-regulatory specific sequences in the promoters of their target genes. In contrast to the genetic code, the transcriptional regulatory code is far from being deciphered and is determined by sequence specificity of TFs, combinatorial cooperation between TFs and chromatin competence. Here we addressed one of these determinants by characterizing the target sequence specificity of 63 plant TFs representing 25 families, using protein-binding microarrays. Remarkably, almost half of these TFs recognized secondary motifs, which in some cases were completely unrelated to the primary element. Analyses of coregulated genes and transcriptomic data from TFs mutants showed the functional significance of over 80% of all identified sequences and of at least one target sequence per TF. Moreover, combining the target sequence information with coexpression analysis we could predict the function of a TF as activator or repressor through a particular DNA sequence. Our data support the correlation between cis-regulatory elements and the sequence determined in vitro using the protein-binding microarray and provides a framework to explore regulatory networks in plants.T ranscription factors (TFs) mediate cellular responses through recognizing specific cis-regulatory DNA sequences at the promoters of their targets genes. In plants, organ development is a continuous process that expands beyond the embryonic phase and, as sessile organisms, plants have to face with a wide range of environmental stresses. Signaling cascades governing developmental and stress switches converge at the gene expression level. Pioneering work (1) suggested that transcriptional regulation may play more important roles in plants than in animals, given the large number of TF-coding genes in plant genomes, ranging from 6% to 10%, depending on the database.During the last few years, the advance in the determination of TF-binding sites, including both in vivo and in vitro techniques, is helping to decipher the transcriptional regulatory code (2-4). In vivo approaches involving immunoprecipitation of TF-bound chromatin followed by microarray or sequencing analysis (ChIPchip and ChIP-seq, respectively) are contributing to the knowledge of the transcriptional networks associated with a TF. ChIP-based techniques revealed that TFs may bind to thousands of genomic fragments, suggesting that the TF is interacting indirectly with DNA or that the binding requires additional cooperative factors (5, 6). The situation may not be different in the case of plant genomes. To date, only a limited number of studies have deepened in the discovery of the targets of some TFs and found that, similar to TFs in animals, TFs in plants bind to hundreds or thousands of DNA fragments; in some cases, only a small proportion of targets respond transcriptionally to the TF, obscuring the identification of actual binding sites (7-9). In this context, the precise identification of the DNA-binding sequence of each TF may be ins...

A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana

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“…10A). This motif can be interpreted as an MBSIIg box (GKTWGGTR; R, A, or G; K, G, or T; W, A, or T; Prouse and Campbell, 2012), similar to those obtained for other plant R2R3 MYBs (Franco-Zorrilla et al, 2014). Given that some R2R3 MYBs also recognize MBSII elements, we evaluated binding to DNA motifs in which the G nucleotide in the sixth position in the GTTAGGT sequence was replaced by a T residue.…”

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