Fig. 4.

Promoter-sequence dependence of primer-dependent initiation: sequences flanking the primer binding site. Sequence logos for primer-dependent initiation at TSS positions 7, 8, and 9 (corresponding to primer binding sites 6 to 7, 7 to 8, and 8 to 9, respectively) in stationary-phase E. coli cells (Left) or in vitro with the dinucleotide primer UpA (Right). The height of each base X at each position Y represents the relative log₂ enrichment (averaged across replicates) of the percent 5′-OH RNAs expressed from promoter sequences containing nontemplate-strand X at position Y. Red, consensus nucleotides; black, nonconsensus nucleotides. Other symbols and colors as in Fig. 1.