Figure 3. Tup1 restricts Rap1 binding through chromatin-modifying co-factors.

A) Genomic loci bound by Tup1 in wildtype cells (red circles) as determined by ChIP-chip (p<0.005, Methods) during growth in the presence of glucose (left) and after glucose had been depleted from the media (right). Rap1 low-glucose targets are indicated by black circles (upper) and the subset of those targets also bound inappropriately in a tup1Δ strain is shown in the lower panel. Tup1 targets indicated in the lower panel are identical to those in the upper panels, and are reproduced for comparison to the respective Rap1 targets. B) Rap1 occupancy in strains lacking the Tup1-associated chromatin modifying proteins Isw2 and Hda1, as determined by ChIP-chip during exponential growth in the presence of glucose (see Figure 2A for details). C) Same as Figure 2B, but for the strains indicated. D) The average mRNA expression change²³,²⁸ (deletion over wildtype) of the genes downstream of 23 low-glucose Rap1 targets and 223 static targets. To avoid ambiguity regarding which gene might be regulated by Rap1, only genes downstream of unidirectional promoters are plotted.