Diversified Evolution of Downstream Transcription Start Sites in Oryza sativa and Arabidopsis thaliana

Abstract

Alternative usage of transcription start sites (TSSs) is one of the key mechanisms to generate gene variation. Here we show diversified evolution of TSSs in Oryza sativa and Arabidopsis thaliana by comprehensive analyses of full-length cDNAs and genome sequences. We determined 45,917 representative TSSs within 23,445 loci of O. sativa and 35,313 TSSs within 16,964 loci of A. thaliana. The nucleotide features around TSSs displayed distinct patterns when the most upstream TSSs were compared to downstream TSSs. In addition, this difference was commonly observed in the two species. Relative entropy analysis revealed that the most upstream TSSs had retained canonical cis-elements, whereas downstream TSSs showed atypical nucleotide features. These results indicate that plant TSSs were generally diversified in downstream regions, which resulted in the development of new gene expression patterns. We discuss the possibility that O. sativa and A. thaliana might have evolved novel TSSs in an independent manner.