Comparative TSS-seq analysis among natural variations of <i>Arabidopsis</i> reveals the genetic stability of genic and nongenic promoters

In a previous TSS-seq analysis, we identified >300 K promoters in the <i>Arabidopsis</i> genome. The majority were nongenic promoters, composed of intragenic, antisense, and orphan promoters. Although several nongenic promoters for biological processes have been identified, the significance of these nongenic promoters is unclear. In this study, we evaluated several characteristics of these promoters, including their genetic stability by analyzing the promoter sequences, peak positions of the TSS clusters using natural variations of <i>Arabidopsis</i>, the expression levels, and promoter structures. The results indicate that nongenic promoters are not genetically stable in the promoter sequence or the TSS peak position, whereas the canonical, genic promoters are stable in both. Together with the less structured features of nongenic promoters, such as core promoter elements and epigenetic traits, the results strongly suggested that the majority of the nongenic promoters do not have biological significance, except for the genetically stable minorities. Interestingly, the genetic stability of the promoters is positively associated with the expression level. In conclusion, our results raised a possibility that the most nongenic promoters result from leaky transcription or transcriptional noise.