Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis

Our limited understanding of plant promoters does not allow us to recognize any core promoter elements for the majority of plant promoters. To understand the promoter architecture of Arabidopsis, we used the combined approach of in silico detection of novel core promoter elements and large-scale determination of transcription start sites (TSSs). To this end, we developed a novel methodology for TSS identification, using a combination of the cap-trapper and massively parallel signature sequencing methods. This technique, CT-MPSS, allowed us to identify 158 237 Arabidopsis TSS tags corresponding to 38 311 TSS loci, which provides an opportunity for quantitative analysis of plant promoters. The expression characteristics of these promoters were analyzed with respect to core promoter elements detected by our in silico analyses, revealing that Arabidopsis promoters contain two main types of elements with exclusive characteristics, the TATA type and the GA type. The TATA-type promoters tend to be associated with the Y Patch and the Inr motif, and cause high expression with sharp-peak TSS clusters. By contrast, the GA type produces broad-type TSS clusters. Unlike mammalian promoters, plant promoters are not associated with CpG islands. However, plant-specific GA-type promoters share some characteristics with mammalian CpG-type promoters.