Statistical Characterization of Transcription Start Sites in Plant Genomes

Although large amounts of genomic and full-length cDNA sequence data from plants are now publicly available, knowledge of the promoters and transcription start sites (TSSs) in plants is still limited compared to mammals, such as human and mouse. In a recent paper, a prominent GC-compositional strand bias or GC-skew (=(C-G)/(C+G)), where C and G denote the numbers of cytosine and guanine residues, was reported near the transcription start sites in Arabidopsis thaliana [6]. However, it is unclear whether other eukaryotic species have equally prominent GC-skews, and the biological meaning of this trait remains unknown. In this study, we conducted comparative analysis using sequences from various eukaryotic genomes animals, fungi, protists, and plants, to statistically characterize TSSs of plant genes. In addition, we explored the potential value of GC-skew as an index for TSS-prediction in plants genomes, where there is a lack of correlation among CpG -islands and genes.