Pho-FLAG and Sce-FLAG binding peaks at PRE2.

(A) A map of the en gene showing the location of the PREs and the probes used for the qPCR (#1–8). (B,C) Results of X-ChIP experiment with Sce-FLAG (B) and Pho-FLAG (C) driven by en-Gal4 (open bars) or ci-Gal4 (closed bars). Pho binding was also done on all chromatin preparations. The results of a representative experiment are shown. These experiments were done with a different batch of FLAG antibody and different ChIP reagents than those done in Fig. 5. Further, 20 larvae were used for each sample instead of 10. Under these conditions, we did not see a difference in the level of binding to the PREs between the “ON” and the “OFF” states; however, the qualitative result, PcG proteins binding to PRE2 in both the “ON” and “OFF” states was the same in these experiments and those in Fig. 5.