Activator occupancy and distal promoter motifs.

<p>(A) UCSC browser view of three pol II (<i>RNU4atac</i>, <i>U1-like-5</i>, and <i>Unknown-6</i>) and one pol III (<i>tRNAU1</i>) gene showing occupancy by the factors indicated on the right of each panel. The chromosome coordinates are shown on top, the genes present in the region and their orientation at bottom. The y axis shows tag counts. (B) Promoter region (−400 to +1) of the four genes depicted in (A) with the positions of the GABPA (GA-motif), ZNF143 (SBS), and POU2F1 (octamer) binding sites found by MEME or MAST indicated. The positions of the PSE and TATA box are also shown, and the promoters were aligned according to the PSE position. The crossed-out motifs have either no corresponding peak of occupancy or are not the closest to the peak summit. The orientation of each motif is indicated with an arrow. (C) LOGOs of the ZNF143, POU2F1 (octamer) and GABP binding motifs generated by WebLogo with the motifs located closest to the corresponding factor peak summits (see alignments in Figures S9, S10, S11).