Fig. 5.

Pol II pausing and distance from transcription initiation. a. Metaplot of TSS-RNAs initiating outside of the exact TSS region +/− 10 bp (greyed out), which was excluded from this analysis. The 5′-ends of RNAs are shown in dashed lines and their 3′-ends in solid lines. RNA initiating at more upstream regions are shown in red and at downstream regions in blue. b. 2-d scatter plot of initiation on two genes with top 20 FPKM values as in [31]. c. TSS-RNA length versus their initiation location around the TSS. Circles show mean (with SEM) for TSS-RNA lengths metaplot for RNAs initiating at the indicated locations (positions) relative to the TSS (vertical line). Grey line (right Y-axis) shows the number of RNAs mapping (metagene) to each location in Replicate 1. d. Weblogo plot of DNA sequence context around locations of Pol II pausing based on distance from the reannotated TSS (top) and relative to 3′-end of each RNA