Transcription factors (TFs) are key nodes of gene regulatory networks
that specify plant morphogenesis and control specific pathways such as stress
responses. TFs directly interact the genome by recognizing specific DNA sequence,
in terms of a complex system to fine-tune spatiotemporal gene expression. The
combinatorial interaction among TFs determines regulatory specificity and defines
the set of target genes to orchestrate their expression during developmental switches.
In this chapter, we provide a catalog of plant-specific TFs and a comprehensive
assessment of whether genome-wide analyses have so far been used for identifying
potential direct target genes for each TFs. We further construct comprehensive
TF-associated regulatory networks in the model plant Arabidopsis thaliana using
genome-wide datasets from our ChIP-Hub database (http://www.chiphub.org/).We
discuss how to dissect the network structure to identify potentially important crossregulatory
loops in the control of developmental switches in plants.
School of Life Sciences, Nanjing University
Nanjing 210023, China