Figure 4. Intragenic distribution of different forms of RNA pol II in RP genes.

(A) The amplicons/probes used for RNA pol II ChIP and run-on analyses of RPS3. (B) ChIP distribution of total RNA pol II (upper panels) and its phosphorylated CTD forms, in Ser5 (second-line panels) and Ser2 (third-line panels) in cells exponentially growing in glucose (blue bars) or galactose (red bars). The averages of four experiments are shown. Error bars represent the standard deviation. (C) Profile of intragenic RNA pol II distribution in RPS3 in glucose in relation to its distribution in galactose and to the levels of RNA pol II present in the promoter region. Data are relative to probe 2 because the probe 1 data are very low, producing high error levels in relative calculations (not shown). (D) The relative distribution of phosphorylated forms of RNA pol II CTD with regard to the total amount measured by ChIP. Note the lower relative levels of phosphorylated forms in glucose and the opposing behaviors along the gene of the Ser2 and Ser5 phosphorylated forms in galactose. (E) Run-on distribution in cells exponentially growing in glucose (blue bars) or galactose (red bars). The averages of two experiments are shown. Results were normalized according to the signal of the probes of PRI2 present on the same filters, as described in Materials and Methods. Error bars represent the standard deviation. (F) The intragenic distribution of RNA pol II in RP genes, measured by ChIP-on-chip using an array of 5′ and 3′ probes of 231 highly expressed genes, is biased toward the 5′ end of the coding region in glucose in relation to the distribution in galactose. (G) Unlike the RP genes, the RiBi genes show almost the same glucose/galactose pattern as the RNA pol II intragenic distribution as the other non RP genes present in the array. Text inserts are as in Figure 1.