Figure 7. Ubx and GAF may regulate common downstream targets.

(A) Multiple motifs were enriched in MEME analysis of sequences pulled down as potential direct targets of Ubx. Many of these motifs resemble previously known motifs for polcomb (a) and Trithorax (b, e) proteins and general RNA polymerase II associated factors Aef1 (c) and Top2 (h). d, f, g and i are the new motifs not related to any known DNA-binding factors. The numbers below each motifs represents their respective E-value derived by MEME, lower E-value represents higher occurrence and significance for each of the motifs in given dataset. (B) GAF ChIP-qPCR showing enrichment for direct targets of Ubx, ebi and hth. Same set of primers were used to detect enrichment as was used for Ubx ChIP-qPCRs (Fig. 1A). bxd and trl regions were used as positive controls. Bar height represent mean enrichment of Test ChIP over mock ChIP and error bars represent deviation from mean enrichment. Three differnet probes within hth, and one probe near ebi all of which were enriched in pulled-down sequecnes, were validated by ChIP-qPCR. (C) Chromatin immunoprecipitation of Ubx from Cbx^Hm/+ wing disc lysate followed by Westerb blot analysis for GAF. ChIP-Western suggests that GAF is associated with Ubx on chromatin. Densitometric analyses using ImageJ suggested a ∼12-fold specific enrichment for GAF in anti-Ubx lane compared to IgG lane.