FIG. 3.

RNAPII strongly accumulates at around position +50 of the junB gene. Control cells or cells stimulated by IL-6 for 15 min were treated with 7.5 mM KMnO₄. Genomic DNA was purified, and unpaired thymine residues in transcription bubbles were mapped by in vivo footprinting with two primer sets. KMnO₄ sensitivity in vivo was compared to the sensitivity of purified single-stranded (ss) or double-stranded (ds) genomic DNA. Lanes 1 and 6 contain genomic DNA partially cleaved at guanine residues. Footprinting with primer set A (lanes 1 to 5) results in higher-resolution mapping of paused sites in a smaller region than that with primer set B (lanes 6 to 10). Signal intensity of the footprinting data for primer set B was obtained with a Storm 860 image analyzer and is presented on the right. The blue and red lines represent the results of uninduced and induced states, respectively. The positions of end-labeled primers are indicated by arrows with asterisks. The numbers on the left indicate the relative positions from the transcription initiation site.