FIG. 1.

The promoters of many unexpressed genes are preloaded with Pol II, which in many cases is prephosphorylated at Ser5 of the CTD. (A) Heat map of ChIP-chip binding analyses for Pol II at the promoters of expressed and unexpressed genes in MCF-7 cells. (B) Averaging of Pol II (blue) and Ser5P (green) promoter ChIP-chip signals for expressed, unexpressed Pol⁻, and unexpressed Pol⁺ genes. (C) Flowchart outlining the identification of promoters where Pol II is regulated at a postrecruitment level. (D) Averaging of Pol II (blue) and Ser5P (green) promoter ChIP-chip signals for unexpressed Pol⁺ genes with classification based on Ser5P status. (E) Gene-specific ChIP analyses of Pol II, TFIIB, and Ser5P binding at TSS (black) and downstream regions (+1 kb) (yellow) for a set of representative genes. Each bar represents the mean plus the standard error of the mean (SEM) (n ≥ 3).