Factor-independent transcription pausing caused by recognition of the RNA–DNA hybrid sequence

Pausing of transcription is an important step of regulation of gene expression in bacteria and eukaryotes. Here we uncover a factor-independent mechanism of transcription pausing, which is determined by the ability of the elongating RNA polymerase to recognize the sequence of the RNA–DNA hybrid. We show that, independently of thermodynamic stability of the elongation complex, RNA polymerase directly ‘senses’ the shape and/or identity of base pairs of the RNA–DNA hybrid. Recognition of the RNA–DNA hybrid sequence delays translocation by RNA polymerase, and thus slows down the nucleotide addition cycle through ‘in pathway’ mechanism. We show that this phenomenon is conserved among bacterial and eukaryotic RNA polymerases, and is involved in regulatory pauses, such as a pause regulating the production of virulence factors in some bacteria and a pause regulating transcription/replication of HIV-1. The results indicate that recognition of RNA–DNA hybrid sequence by multi-subunit RNA polymerases is involved in transcription regulation and may determine the overall rate of transcription elongation.