The sigma subunit of RNA polymerase contacts the leading ends of transcripts 9-13 bases long on the lambda PR promoter but not on T7 A1.

The sigma subunit of RNA polymerase is responsible for specific initiation of RNA synthesis at promoter sites on DNA. sigma dissociates shortly after initiation. Photoaffinity-labeling experiments performed on transcription complexes with two different DNA promoters, which have highly homologous control sequences upstream from the transcribed regions, have revealed that the sigma subunit of RNA polymerase is contacted by the 5' ends of quite different lengths of nascent RNA in each transcription complex. On the other hand, the labeling of subunits beta beta' is quite similar for both promoters, and the alpha subunit is not labeled in either case. The results of transcription experiments on the phage lambda PR promoter show that sigma can be photoaffinity labeled by RNA chains that are 9-13 nucleotides long and thus remains associated with the core enzyme at least to that point. But on the A1 promoter of phage T7 DNA, photoaffinity labeling of sigma ceases with the trinucleotide. Thus release of sigma from the vicinity of nascent RNA depends not merely on the length but on the sequence of the transcript. For the T7 A1 promoter, sigma labeling ceases while the leading end of the RNA is still base paired to the DNA template; thus, it appears that there is at least one site on the enzyme that interacts with the growing transcript/template hybrid, in a sequence-dependent way, to effect sigma release.(ABSTRACT TRUNCATED AT 250 WORDS)