Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

Significance Primer-dependent transcription initiation—the use of RNA primers as initiating entities in transcription initiation—yields RNA products having a 5′-hydroxyl. Here, we show that primer-dependent initiation in vivo inEscherichia coli involves predominantly dinucleotide primers, involves any of the 16 possible dinucleotide primers, and depends on promoter sequences in, upstream, and downstream of the primer binding site. Crystal structures explain the structural basis of sequence dependence at the promoter position immediately upstream of the primer binding site, namely, interchain base stacking between the promoter template-strand nucleotide and primer 5′ nucleotide. Taken together, our findings provide a mechanistic and structural description of primer-dependent initiation inE. coli .