Figure 8.

Global effects of Mot1 on TBP and TFIIB genomic distribution and correlations with transcription. Plots of average TBP (A) and average TFIIB chromatin (B) occupancies obtained by aligning all annotated Pol II genes with respect to the transcription start site (TSS). The signals were smoothed over a 50-bp sliding window (WT, solid curves; mot1-42, dashed curves). In both cases, the differences in the distributions are highly significant as determined by the Kolmogorov-Smirnov test (P-values as indicated). (C) The heat map displays the transcriptome-wide relationship between TBP occupancy (x-axis), TFIIB occupancy (y-axis), and RNA level (color) in WT cells. Each box represents one or more genes whose TBP and TFIIB occupancies fall within the box's x-axis/y-axis values. The box color is the relative median expression value on a scale defined by the range of all medians in the data set. Note the general trend that increasing TBP and TFIIB promoter occupancy is correlated with increasing RNA level (arrow). However, the correlation between TFIIB and RNA levels is better because there are genes with high TBP occupancy but low expression (black rectangle). (D) The heat map is similar to that in panel C but shows the transcriptome-wide relationship between the differential TBP signal (x-axis), the differential TFIIB signal (y-axis), and the change in RNA level (color) in mot1-42 versus WT cells. As in C, changes in TFIIB occupancy are reasonably well correlated with changes in transcription, whereas changes in TBP promoter occupancy do not correlate as well with changes in RNA level. (E,F) Density distributions of the differential TBP and differential TFIIB signals (as indicated), over the promoters for all the genes. The plots show that in mot1-42 cells compared with WT, TBP occupancies increased at the majority of promoters. In contrast, TFIIB occupancies increased or decreased at roughly equal numbers of promoters, consistent with changes in gene expression in both positive and negative directions.