Time course analysis of Yap1 promoter occupancy after benomyl addition in the growth medium of wild type strain

Growth conditions in the presence of benomyl were strictly identical to those used to follow genome expression. Cells were harvested treated with formaldehyde and lysed with glass beads; the extracts were sonicated to produce chromatin fragments of about 500 bp. Aliquots were immunoprecipitated with HA antibodies and DNA was extracted from the immunoprecipitate (IP) after reversing the cross-links. DNA was extracted directly from another aliquot of chromatin to serve as the input (Inp) control. A 1000 fold dilution of the input and the undiluted IP samples were PCR amplified using primers for the different promoters (see Materials and Methods). Quantitative PCR amplifications were conducted as indicated in Materials and Methods. Enrichment ratio were calculated by taking the zero time benomyl addition as a reference. Three totally independent experiments were conducted for each point and the mean values with standard errors are represented. Note that the negative control gene which do not contain Yap1 motif in their promoter ACT1 exhibit a weak signal which is time independent. On the other hand all the other genes contain a Yap1 motif but some of them (SOD1, CCP1, TSA1) are not up-regulated during the transient benomyl activation.