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. Author manuscript; available in PMC: 2012 Jun 26.
Published in final edited form as: Mol Cell. 2011 Jun 24;42(6):817–825. doi: 10.1016/j.molcel.2011.06.005

Figure 2. Priming of transcription initiation with 2- to 4-nt RNAs can alter the TSS in vitro.

Figure 2

Top shows galP1/cons promoter sequences extending from position −5 to +3 (the galP1/cons promoter is a derivative of the E. coli galP1 promoter with a consensus extended −10 element). Bottom shows results of primer extension analysis of RNA transcripts produced during in vitro transcription assays performed using a DNA fragment containing the galP1/cons promoter (10 nM). Assays were done using P. aeruginosa RNAP (50 nM) in the presence of 100 µM NTPs in the absence (−) or presence of 100 µM of the indicated 2- to 4-nt RNA (see Supplemental Information for details). The position of the 5′ and 3′ end of each small RNA is indicated below the gel along with the percentage of transcripts shifted by each RNA (averages of duplicate measurements). Highlighted in red are RNAs that effectively compete with NTPs and shift the TSS of >10% of transcripts initiated from galP1/cons.