Figure 6.

Gene ontology analysis shows that genes with PPEP are enriched in genes involved in development, reproduction and the response to stimulus. (a) Query of the Gene Ontology database with a list of 1,014 genes with PPEP reveals major biological processes that were significantly overrepresented on this gene list (at a P value cutoff < 0.001). Shown are the number of genes in each Gene Ontology class, the percentage of total genes within each class that have PPEP and the associated P value. (b) Pol II (anti-Rpb3) ChIP data from three UV-inducible genes with PPEP and eIF-5c as a control, comparing Pol II distribution under uninduced and induced conditions (120 mJ/cm² UV exposure followed by a 4-h recovery). After UV irradiation, the ratio of Pol II occupancy detected at the promoter versus downstream primer pair decreases substantially (from a ratio of 13.6 to 4.0 for W, from 16.5 to 7.7 for Hsp70 and from 4.9 to 2.1 for CG12171). n = 2 independent ChIP samples; error bars represent the range. (c) In vivo permanganate footprinting of W and CG12171 before and after UV induction, shown as in Figure 4.