Figure 2.

Effects of ectopic production of a nanoRNase on transcription start site selection. (A) Analysis of transcription start sites during the exponential phase of growth. Average percentage of all transcripts initiated at positions −3 to +3 for the 270 promoters listed in Supplemental Table 1 as determined by high-throughput sequencing. Analysis was performed using RNA transcripts isolated from E. coli cells during the exponential phase of growth that harbored an empty plasmid (wt) or a plasmid that specifies production of E. coli Orn, B. subtilis NrnB, or NrnB^DHH. Plotted are the mean + SD derived from two independent measurements. (B,C) Analysis of transcription start sites during the stationary phase of growth. Average percentage of all transcripts (B) or 5′ triphosphate-carrying transcripts (C) initiated at positions −3 to +3 for the seven promoters with start sites that were significantly affected by ectopic production of a nanoRNase (Supplemental Table 3) as determined by high-throughput sequencing. Analysis was performed using RNA transcripts isolated from E. coli cells during the stationary phase of growth that harbored an empty plasmid (wt) or a plasmid that specifies production of E. coli Orn, B. subtilis NrnB, or NrnB^DHH. Plotted are the mean + SD derived from two independent measurements. (D) Average percentage of all transcripts (all), 5′ triphosphate-carrying transcripts (ppp), 5′ monophosphate-carrying transcripts (p), or 5′ hydroxyl-carrying transcripts (OH) initiated at positions −3 to +3 for the four promoters listed in Supplemental Table 4 as determined by high-throughput sequencing. Analysis was performed using RNA transcripts isolated from E. coli cells during the stationary phase of growth that harbored an empty plasmid. Plotted are the mean + SD derived from two independent measurements.