Motif analysis of TR4 binding sites. (A) Sequences for TR4 binding sites located within 1 kb upstream and downstream of a TSS were retrieved. Significantly overrepresented motifs within TR4 binding sites were identified by MEME. The number of targets is indicated in parenthesis. E-values indicate significance of a given motif. Pie charts show occurrence of DR1 alone, ETS alone, DR1 and ETS, and neither of these motifs within TR4 binding sites. (B) DR1 motif and ETS core motif are depicted in either orientation. Occurrence of DR1 and ETS motifs relative to TR4 peak center in HeLa cells is shown in a histogram. Peak frequency is plotted along the y axis; distance from the peak center is plotted on the x axis. Similar results were obtained with the other 3 cell types, histograms are not shown.