title: A Maize Gene Regulatory Network for Phenolic Metabolism.
abstract: The translation of the genotype into phenotype, represented for example by the expression of genes encoding 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 networks (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 carried out using gene- or TF-centered approaches. In this study, we employed a gene-centered approach utilizing 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 general 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 information derived from TF-centered approaches provides a foundation for a phenolics GRN characterized by interlaced feed-forward loops that link developmental regulators with biosynthetic genes.
authors.affiliation: Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Fan
authors.initials: F
authors.lastname: Yang
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Nan
authors.initials: N
authors.lastname: Jiang
authors.affiliation: Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Haidong
authors.initials: H
authors.lastname: Yu
authors.affiliation: Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Kengo
authors.initials: K
authors.lastname: Morohashi
authors.affiliation: Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology (MCDB) Graduate Program, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Wilberforce Zachary
authors.initials: WZ
authors.lastname: Ouma
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Morales-Mantilla
authors.affiliation: Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Fabio Andres
authors.initials: FA
authors.lastname: Gomez-Cano
authors.affiliation: Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Mukundi
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Luis Daniel
authors.initials: LD
authors.lastname: Prada-Salcedo
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Roberto Alers
authors.initials: RA
authors.lastname: Velazquez
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Jasmin
authors.initials: J
authors.lastname: Valentin
authors.affiliation: Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Maria Katherine
authors.initials: MK
authors.lastname: Mejía-Guerra
authors.affiliation: Department of Biological Sciences, University of Toledo, Toledo, OH 43560, USA.
authors.forename: John
authors.initials: J
authors.lastname: Gray
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Andrea I
authors.initials: AI
authors.lastname: Doseff
authors.affiliation: Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA. Electronic address: grotewold.1@osu.edu.
authors.forename: Erich
authors.initials: E
authors.lastname: Grotewold
mesh_terms: D047369:Chromatin Immunoprecipitation; D005786:Gene Expression Regulation / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics; D010636:Phenols / Q000378:metabolism*; D010666:Phenylpropionates / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism*
chemical_list: D010636:Phenols; D010666:Phenylpropionates; D010940:Plant Proteins; D014157:Transcription Factors
keywords: chromatin immunoprecipitation; flavonoid; phenylpropanoid; yeast one-hybrid