Figure 4. Uncorrected Tup1 differential binding targets misleadingly indicate that Tup1 is primarily a transcriptional activator.

Scatter plots show the differential transcriptional activation after rapamycin treatment as blue points. Differential RNAPII Ser5P occupancy before and after rapamycin treatment was measured by ChIP-seq and plotted on the X-axis. Differential mRNA expression levels in the same cultures were measured using microarrays and plotted on the Y-axis, in scatter plots showing 4929 genes. We used MACS to identify differential binding targets (DBTs) of Tup1 as described in the text and plotted them on the same plots in red. (A) The top 100 DBT peaks ranked by fold change were assigned to 55 ORFs, which are plotted in red. (B) The top 500 DBT peaks were assigned to 295 ORFs, which are plotted in red. Tup1 DBT ORFs tended to be upregulated genes in response to rapamycin.