Structural and mechanistic basis of sigma-dependent transcriptional pausing

Using site-specific protein-DNA photocrosslinking, high-throughput sequencing, and cryo-EM structure determination, we show directly that sigma-dependent pausing involves DNA scrunching, we define a consensus sequence for formation of a stable scrunched paused complex that is identical to the consensus sequence for pausing in initial transcription, and we identify positions of DNA scrunching on DNA nontemplate and template strands. Our results illuminate the structural and mechanistic basis of sigma-dependent transcriptional pausing.