Gene

Cell biology

Linguistics

Philosophy

Biology

General transcription factor

RNA polymerase II

Transcription (linguistics)

Promoter

Computational biology

Bacterial transcription

Transcription factor II F

Genetics

Riboswitch

Non-coding RNA

Transcription factor

Chemistry

Biophysics

RNA polymerase

Gene expression

Proceedings of the National Academy of Sciences

Significance Transcriptional pausing by RNA polymerases (RNAPs) is critical for genetic regulation, yet how RNA structures modulate this universal process is poorly understood. Combining biochemical and single-molecule fluorescence approaches, we here uncover a dynamic interplay between nascent messenger RNA structure and transcription factor NusA in modulating transcriptional pausing. Transcription factor NusA binds highly reversibly to the elongation complex to fine-tune the transcription rate. We find that ligand-induced riboswitch folding within the RNAP exit channel promotes transcriptional pausing, whereas it prevents NusA recruitment to the paused elongation complex. Taken together, our data reveal a dynamic model of transcription factor trafficking mediated by RNA cotranscriptional folding, expanding our understanding of the general transcription process.

Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation