Exploring Plant Transcription Factor Regulatory Networks

Yu R, Chen D
J Integr Bioinform. 2019 Sep 13;16(3):20192001. doi: 10.1515/jib-2019-2001. PMID: 31560650

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.

Cover image


School of Life Sciences, Nanjing University
Nanjing 210023, China

Back to top