FIGURE 1.

MATα is a poorly active gene in comparison to a highly active ADH1 gene. A, RT-PCR analysis of ADH1 and MATα mRNAs. Yeast cells were grown in YPR as well as YPG. Total RNA was prepared from harvested culture and analyzed for ADH1 and MATα mRNAs. The level of ADH1 mRNA was set to 100, and MATα mRNA was normalized with respect to 100. Normalized mRNA levels are plotted in the form of a histogram. B, analysis of RNA polymerase II association with the ADH1 and MATα loci. Yeast cells were grown in YPR as well as YPG and cross-linked by formaldehyde. Immunoprecipitation was performed as described previously (41–44) using a mouse monoclonal antibody 8WG16 (Covance) against the carboxyl terminal domain of the largest subunit (Rpb1p) of RNA polymerase II. Immunoprecipitated DNAs were analyzed by PCR using the primer pairs targeted to ADH1 and MATα. The ratio of the PCR signal of immunoprecipitated DNA to that of input DNA was determined and referred to as the ChIP signal. The ChIP signal at ADH1 was set to 100, and the ChIP signals at MATα and Chr-V were normalized with respect to 100. The normalized ChIP signals (represented as normalized occupancy) are plotted in the form of a histogram.