title: Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites.
abstract: Core promoters are crucial for gene regulation, providing blueprints for the assembly of transcriptional machinery at transcription start sites (TSSs). Empirically, TSSs define the coordinates of core promoters and other regulatory sequences. Thus, experimental TSS identification provides an essential step in the characterization of promoters and their features. Here, we describe the application of CAGE (cap analysis of gene expression) to identify genome-wide TSSs used in root and shoot tissues of two maize (Zea mays) inbred lines (B73 and Mo17). Our studies indicate that most TSS clusters are sharp in maize, similar to mice, but distinct from Arabidopsis thaliana, Drosophila melanogaster, or zebra fish, in which a majority of genes have broad-shaped TSS clusters. We established that ∼38% of maize promoters are characterized by a broader TATA-motif consensus, and this motif is significantly enriched in genes with sharp TSSs. A noteworthy plasticity in TSS usage between tissues and inbreds was uncovered, with ∼1500 genes showing significantly different dominant TSSs, sometimes affecting protein sequence by providing alternate translation initiation codons. We experimentally characterized instances in which this differential TSS utilization results in protein isoforms with additional domains or targeted to distinct subcellular compartments. These results provide important insights into TSS selection and gene expression in an agronomically important crop.
authors.affiliation: Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Molecular Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210.
authors.forename: María Katherine
authors.identifier: http://orcid.org/0000-0002-2791-182X
authors.initials: MK
authors.lastname: Mejía-Guerra
authors.affiliation: Department of Physiology and Cell Biology, 305B Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Instituto de Investigación en Microbiología y Biotecnología Agroindustrial, Universidad Católica de Manizales, Carrera 23 No 60-63 Manizales, Colombia.
authors.forename: Narmer F
authors.identifier: http://orcid.org/0000-0002-8337-2824
authors.initials: NF
authors.lastname: Galeano
authors.affiliation: Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Mabel
authors.initials: M
authors.lastname: Vidal
authors.affiliation: Department of Biological Sciences, University of Toledo, Toledo, Ohio 43606.
authors.forename: John
authors.initials: J
authors.lastname: Gray
authors.affiliation: Department of Physiology and Cell Biology, 305B Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210 doseff.1@osu.edu grotewold.1@osu.edu.
authors.forename: Andrea I
authors.initials: AI
authors.lastname: Doseff
authors.affiliation: Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210 Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210 doseff.1@osu.edu grotewold.1@osu.edu.
authors.forename: Erich
authors.initials: E
authors.lastname: Grotewold
mesh_terms: D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D059372:Nucleotide Motifs; D018517:Plant Roots / Q000166:cytology / Q000235:genetics; D018520:Plant Shoots / Q000166:cytology / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site; D003313:Zea mays / Q000166:cytology / Q000235:genetics*