Maize Gene Regulatory Network for Phenolic Metabolism

• Published in: Molecular plant Vol. 10; no. 3; pp. 498 - 515
• Main Authors: Yang, Fan, Li, Wei, Jiang, Nan, Yu, Haidong, Morohashi, Kengo, Ouma, Wilberforce Zachary, Morales-Mantilla, Daniel E, Gomez-Cano, Fabio Andres, Mukundi, Eric, Prada-Salcedo, Luis Daniel, Velazquez, Roberto Alers, Valentin, Jasmin, Mejía-Guerra, Maria Katherine, Gray, John, Doseff, Andrea I, Grotewold, Erich
• Format: Journal Article
• Language: English
• Published: England Elsevier Inc 06-03-2017
• Subjects: Chromatin Immunoprecipitation; flavonoid; Gene Expression Regulation - genetics; Gene Regulatory Networks - genetics; Phenols - metabolism; phenylpropanoid; Phenylpropionates - metabolism; Plant Proteins - genetics; Plant Proteins - metabolism; Transcription Factors - genetics; Transcription Factors - metabolism; yeast one-hybrid; Zea mays - genetics; Zea mays - metabolism; 代谢; 基因启动子; 基因调控网络; 植物化学物质; 玉米; 生物合成基因; 转录因子; 酚类化合物; phenylpropanoid; flavonoid; yeast one-hybrid; chromatin immunoprecipitation
• ISSN: 1674-2052; 1752-9867
• DOI: 10.1016/j.molp.2016.10.020

The translation of the genotype into phenotype, represented for example by the expression of genes encod- ing enzymes required for the biosynthesis of phytochemicals that are important for interaction of plants with the environment, is largely carried out by transcription factors （TFs） that recognize specific cis-regulatory elements in the genes that they control. TFs and their target genes are organized in gene regulatory net- works （GRNs）, and thus uncovering GRN architecture presents an important biological challenge necessary to explain gene regulation. Linking TFs to the genes they control, central to understanding GRNs, can be car- ried out using gene- or TF-centered approaches. In this study, we employed a gene-centered approach uti- lizing the yeast one-hybrid assay to generate a network of protein-DNA interactions that participate in the transcriptional control of genes involved in the biosynthesis of maize phenolic compounds including gen- eral phenylpropanoids, lignins, and flavonoids. We identified 1100 protein-DNA interactions involving 54 phenolic gene promoters and 568 TFs. A set of 11 TFs recognized 10 or more promoters, suggesting a role in coordinating pathway gene expression. The integration of the gene-centered network with informa- tion derived from TF-centered approaches provides a foundation for a phenolics GRN characterized by in- terlaced feed-forward loops that link developmental regulators with biosynthetic genes.