Figure 2. Differential Binding of Pax7 and Pax3 to Homeo-box and Paired Motifs.

(A–B) Pax7 and Pax3 binding sites obtained from ChTAP-seq are enriched for homeobox (hbox) and paired (prd) motifs. Consensus sequence of hbox and prd motif obtained from MEME (Bailey et al., 2009) analysis of the top 500 Pax3/Pax7 peaks, ranked based on MACS (Zhang et al., 2008) scores. MEME search was restricted to a 50 base pair window around peak summit. See Figure S2 for a description of ChTAP and validation of a subset of targets.

(C) Pax7 peaks were ranked based on MACS scores. Peaks were binned into groups of 100. A single bar represents each bin. The fraction of peaks containing prd, hbox or both prd/hbox was determined by FIMO (Grant et al., 2011) using the PWM obtained from MEME suite above from the scan of 200 base pairs around the peak summit. (D) Similar analysis of Pax7 unique peaks also showed that hbox motif is highly enriched in this peak subset. (E–F) The relative distribution of prd and hbox motifs in Pax3 and Pax3 unique peaks. Pax3 peaks have a higher proportion of prd to hbox compared to Pax7. (G) Box plots visualizing fraction of peaks containing hbox motif for Pax3 and Pax7 total peaks. Peaks were ranked based on MACS scores and binned into 100-peak groups. The fraction of peaks within each 100-peak group containing the hbox motif was calculated based on the FIMO analysis as describe earlier. Data was transformed into percentiles. Wilcoxon Rank-Sum test shows that the mean fraction peaks containing hbox motif is significantly higher in Pax7 dataset compared to Pax3. Dashed red line represents the mean; solid black line inside the box represent median. Lower and upper solid circles represent the 5^th and the 95^th percentiles respectively. (H) Similar analysis as in G showing that the fraction of Pax3 peaks containing prd motif is significantly higher than those of Pax7.