PUBLICATION
Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites
- Authors
- Mejía-Guerra, M.K., Li, W., Galeano, N.F., Vidal, M., Gray, J., Doseff, A.I., Grotewold, E.
- ID
- ZDB-PUB-160216-15
- Date
- 2015
- Source
- The Plant cell 27: 3309-20 (Journal)
- Registered Authors
- Li, Wei
- Keywords
- none
- MeSH Terms
-
- Gene Expression Regulation, Plant*
- Gene Library
- Genome, Plant/genetics*
- Genotype
- Nucleotide Motifs
- Plant Roots/cytology
- Plant Roots/genetics
- Plant Shoots/cytology
- Plant Shoots/genetics
- Promoter Regions, Genetic/genetics*
- Sequence Analysis, RNA
- Transcription Initiation Site*
- Zea mays/cytology
- Zea mays/genetics*
- PubMed
- 26628745 Full text @ Plant Cell
Citation
Mejía-Guerra, M.K., Li, W., Galeano, N.F., Vidal, M., Gray, J., Doseff, A.I., Grotewold, E. (2015) Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites. The Plant cell. 27:3309-20.
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.
Errata / Notes
This article is corrected by ZDB-PUB-220906-238 .
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping