Figure 3

MyoD has a similar E-box preference for both endogenous and overexpressed MyoD. (A) Overexpressed MyoD (lenti) and endogenous MyoD (primary.tube) have similar E-box distributions. We collected all genomic E-boxes (excluding sex chromosomes and those present in the peaks of the control samples) and ranked them based on p-values for the read coverage at the E-boxes. We partitioned them into bins of top 1K, top 1001 to 10K, etc., until all E-boxes are included. Within each bin, we calculated the percentage of each type of E-box variant, and plotted the distribution. The background E-box distribution over the entire genome is also included as a reference. (B) MYOD binding sites for overexpressed MyoD (lenti) and endogenous MyoD (primary.tube) share the same sequence preference. We used motif discovery to identify the E-box motif under MyoD bound peaks for the top 35K, the top 35K+1 to 70K peaks, and the top 70K+1 to 110K peaks. The E-box sequence preferences are nearly identical, including within the flanking regions. Motifs in lower ranking peaks tend to have slightly more sequence degeneracy. (C) MyoD E-box average PWM score compared to peak rank. The MyoD PWM is derived from our previous study [4]. Weak peaks tend to have weaker motifs, but the degradation is more gradual for overexpressed MyoD peaks (lenti) beyond the top 67K, suggesting that a subset of noisy low peaks in the endogenous MyoD (primary.tube) is elevated to reasonably strong peaks distinguished from the background. X-axis: the peak rank bins. Y-axis: the average PWM scores for all peaks within the rank bin.