Figure 3

Transcription initiation in S. elongatus. (a) AT content of the transcription start. The AT content from -200 to +200 from the start site of transcription was averaged for all mRNAs. A strong enrichment in AT content is observed at the -10 element as well as a strong preference for adenine at the first nucleotide of a transcript. (b) -10 element consensus logo. A consensus -10 element similar in sequence to that determined for E. coli was identified through sequence alignment (Materials and methods). (c) Normalized RNA pol occupancy at promoter. For each of the top 500 expressed mRNAs, the RNA pol occupancy was normalized to a mean occupancy of 0.5 per nucleotide, and then averaged across mRNAs from -500 to +500. A peak in RNA pol occupancy is observed, on average, 63 nucleotides within the RNA transcript, suggesting potential stalling of RNA pol after initiation of transcription rather than at the promoter. (d) RNA pol retention ratio at the promoter is variable. The relative amount of RNA pol at the 5' end versus RNA pol in the ORF varies from transcript to transcript. RNA pol at the 5' end was calculated as the mean occupancy in a 200-nucleotide window centered at the +63 nucleotide. RNA pol transcribing was calculated as the mean occupancy in a 200-nucleotide window centered in the middle of the first ORF.