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Plant Cell. 2015 Dec;27(12):3309-20. doi: 10.1105/tpc.15.00630. Epub 2015 Dec 1.

Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites.

Author information

1
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.
2
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.
3
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.
4
Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210.
5
Department of Biological Sciences, University of Toledo, Toledo, Ohio 43606.
6
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.
7
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.

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.

PMID:
26628745
PMCID:
PMC4707454
DOI:
10.1105/tpc.15.00630
[Indexed for MEDLINE]
Free PMC Article

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