Figure Legend Snippet: KEY RESOURCES TABLE

Techniques Used: Flow Cytometry, shRNA, Recombinant, Plasmid Preparation, Western Blot, Electron Microscopy, Activation Assay, DNA Purification, SYBR Green Assay, Endotoxin Assay, Software, Cell Counting, Staining

Fig. 2 A ) attenuates USER digestion. TECs prepared under conditions that predominantly yield slow-migrating complexes ( Fig. 4 B , lane 2) inhibit USER digestion, indicating promoter occupation by open complexes. TECs prepared under conditions that yield >97% fast-migrating complexes ( Fig. 4 B , lane 6) are efficiently digested, indicating the absence of open complexes. The grayscale on the lower cut-out is adjusted to better show the RNA band; the full gel is shown with this darker grayscale setting in Fig. S6 D . C , quantification of USER digestion for key lanes from panel B as the ratio of USER digested to full-length band intensity. The gel shown in panel B is representative of two independent replicates. TEC, transcription elongation complex. " title="USER footprinting to assess promoter accessibility. A , structure ..." property="contentUrl" width="100%" height="100%"/>
Figure Legend Snippet: USER footprinting to assess promoter accessibility. A , structure of Thermus aquaticus initiation complex (PDB: 4XLN) annotated to indicate the position of P RA1 dU bases relative to direct contacts between σ and promoter DNA. B , USER footprinting assay to assess P RA1 promoter accessibility. Saturation of the P RA1 promoter with open complexes (conditions from Fig. 2 A ) attenuates USER digestion. TECs prepared under conditions that predominantly yield slow-migrating complexes ( Fig. 4 B , lane 2) inhibit USER digestion, indicating promoter occupation by open complexes. TECs prepared under conditions that yield >97% fast-migrating complexes ( Fig. 4 B , lane 6) are efficiently digested, indicating the absence of open complexes. The grayscale on the lower cut-out is adjusted to better show the RNA band; the full gel is shown with this darker grayscale setting in Fig. S6 D . C , quantification of USER digestion for key lanes from panel B as the ratio of USER digested to full-length band intensity. The gel shown in panel B is representative of two independent replicates. TEC, transcription elongation complex.

Techniques Used: Footprinting