Fig. 5.—

The impact of GC content and TATA box on gene transcription divergence. (A) Comparison of the GC content in 1 kb sequences upstream of genes with the cis or trans effects. The GC content was calculated by sliding a 400 bp window with the step size of 1 bp on the upstream sequences. Both the cis and trans genes have higher GC contents in the upstream sequences than the conserved genes (P = 3.40E−64). The enhancing CT genes had the highest GC content (P = 2.82E−40). (B) The association between the TATA box and the transcription divergence between two species. Genes were sorted based on their transcription divergence between two parental strains and a sliding window of 250 genes with the step size of one gene was used to calculate the transcription divergence and the percentage of genes with the TATA boxes. The TATA box is enriched in both the trans (P = 4.15E−14) and cis genes (P = 2.88E−12). The percentage of CT genes with the TATA box remained constant, regardless of the level of gene transcription divergence between species, whereas that in the cis or trans only genes tend to be increasingly associated with the level of gene transcription divergence. Different window sizes and steps sizes in the analysis lead to similar conclusions in both A and B (data not shown).