| Summary: | 博士 === 國立陽明大學 === 生物醫學資訊研究所 === 103 === Gene expression evolution occurs through changes in cis- or trans-regulatory elements or both. As cis and trans regulation operate through different molecular mechanisms, cis and trans mutations may show different inheritance patterns and may be subjected to different selective constraints. To investigate these issues, I analyzed gene expression data from two Saccharomyces cerevisiae strains and their hybrid, obtained with high-throughput sequencing. The data indicate that compared to other types of genes, those with antagonistic cis-trans interactions are more likely to exhibit over- or under-dominant inheritance of expression level. Moreover, in accordance with previous studies, genes with trans variants tend to have a dominant inheritance pattern, while cis variants are enriched for additive inheritance. In addition, cis regulatory differences contribute more to expression differences between species than within species, whereas trans regulatory differences show a stronger association between divergence and polymorphism. Our data indicate that in the trans component of gene expression differences genes subjected to weaker selective constraints tend to have an excess of polymorphism over divergence compared to those subjected to stronger selective constraints. In contrast, in the cis component, this difference between genes under stronger and weaker selective constraint is mostly absent. To explain these observations, I propose that purifying selection more strongly shapes trans changes than cis changes and that positive selection may have significantly contributed to cis regulatory divergence.
Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. For this reason I investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. I divided promoters into the proximal regions and the distal regions, which are defined, respectively, as the 200bp region upstream of the transcription starting site (TSS) and as the 200bp region upstream of the proximal region. Predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, S. cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments. Differences in TFBSs correlate with the cis component of gene expression differences between S. cerevisiae and its sister species S. paradoxus, as well as between the two closely related S. cerevisiae strains used in our hybrid experiments.
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