biostudies-literatureChauvier AHHS | National Institutes of HealthNIGMS NIH HHSe2109026118https://www.ebi.ac.uk/biostudies/studies/S-EPMC8617461biostudies-literatureUnknown118(47)Cotranscriptional RNA folding is widely assumed to influence the timely control of gene expression, but our understanding remains limited. In bacteria, the fluoride (F^-)-sensing riboswitch is a transcriptional control element essential to defend against toxic F^- levels. Using this model riboswitch, we find that its ligand F^- and essential bacterial transcription factor NusA compete to bind the cotranscriptionally folding RNA, opposing each other's modulation of downstream pausing and termination by RNA polymerase. Single-molecule fluorescence assays probing active transcription elongation complexes discover that NusA unexpectedly binds highly reversibly, frequently interrogating the complex for emerging, cotranscriptionally folding RNA duplexes. NusA thus fProceedings of the National Academy of Sciences of the United States of AmericaDynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation.PMC8617461R01 GM118524R35 GM131922GM062357GM131922GM118524R01 GM062357Walter NGAjmera PChauvier AYadav RfalseDynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation.Cotranscriptional RNA folding is widely assumed to influence the timely control of gene expression, but our understanding remains limited. In bacteria, the fluoride (F^-)-sensing riboswitch is a transcriptional control element essential to defend against toxic F^- levels. Using this model riboswitch, we find that its ligand F^- and essential bacterial transcription factor NusA compete to bind the cotranscriptionally folding RNA, opposing each other's modulation of downstream pausing and termination by RNA polymerase. Single-molecule fluorescence assays probing active transcription elongation complexes discover that NusA unexpectedly binds highly reversibly, frequently interrogating the complex for emerging, cotranscriptionally folding RNA duplexes. NusA thus f2021-01-01T00:00:00Z2021 Nov2025-04-04T07:51:15.483Z2025-04-04T07:51:15.483ZS-EPMC86174613478246210.1073/pnas.2109026118