期刊
PLANT CELL
卷 27, 期 12, 页码 3309-3320出版社
AMER SOC PLANT BIOLOGISTS
DOI: 10.1105/tpc.15.00630
关键词
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资金
- National Science Foundation [IOS-1125620]
- Ohio Plant Biotechnology Consortium through the Ohio Agricultural Research and Development Center [OPBC2014-009]
- Center for Applied Plant Sciences Computational Biology Laboratory
- Division Of Integrative Organismal Systems
- Direct For Biological Sciences [1125620] Funding Source: National Science Foundation
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 similar to 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 similar to 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.
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