Comparative TSS-seq analysis among Arabidopsis natural variations revealed genetic stability of genic and non-genic promoters

In our previous study, more than 300K promoters were identified in the Arabidopsis genome, including many non-genic promoters that do not transcribe gene bodies. Although some functional non-genic promoters have been reported, the biological importance of many others remains unclear. In this study, we evaluated their genetic stability by analysis of promoter sequence and peak positions of TSS clusters using Arabidopsis natural variations. Canonical genic promoters showed high conservation of sequence and TSS peak positions. Moreover, they were well structured in terms of the presence of core elements, promoter context, and epigenetic features. These data revealed that the genic promoters are genetically stable and well-structured, which is consistent with their biological significance for the expression of genes. On the other hand, non-genic promoters showed low stability of TSS peak position and low structured features. Therefore, We concluded that most non-genic promoters are biologically insignificant with some exceptions. Interestingly, the genetic stability of promoters has a positive relation with the expression level. This suggests weak promoters like most non-genic promoters are results of leaky transcription, which supports the concept of “transcriptional noise”. Overall design: CAGE-seq profiling of two-weeks Arabidopsis 4 accessions(Altenb-2, Kly-1, Shigu-2, and Vash-1) under high light + cold stress condition and control condition