Genomic Study of RNA Polymerase II and III SNAPc-Bound Promoters Reveals a Gene Transcribed by Both Enzymes and a Broad Use of Common Activators
Figure 2
SNAPc subunits occupancy and proximal promoter motifs.
(A) UCSC browser views of a pol III (tRNAU1) and a pol II (RNU4atac) gene showing occupancy by the factors indicated on the left. 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) Two examples of non-annotated genomic regions showing occupancy by SNAPc subunits, GTF2B, and POLR2B. (C) Box plot of BRF2, GTF2B, and SNAPc subunit positions. For each gene, the position of the peak summit for each SNAPc subunit relative to the TSS (set at 0) was determined. A median position (black bars in boxes, number in brackets on the y axis) was calculated. For the pol II genes, only the upper two tertiles of each SNAPc subunit and GTF2B scores were included. The position for each gene is represented by a circle. (D) LOGOs of PSE and TATA box generated by WebLogo with the motifs identified with MEME (alignments in Figures S4 and S5). The top panel shows the PSE LOGO for pol II snRNA genes, the middle panel shows the PSE LOGO for pol III genes, and the bottom panel shows the TATA box LOGO for pol III genes.