Monitoring RNA dynamics in native transcriptional complexes

Adrien Chauvier, Patrick St-Pierre, Jean-Francois Nadon, Elsa Hien, Daniel Cibran Perez Gonzalez, Sebastien H. Eschbach, Anne-Marie Lamontagne, Carlos Penedo *, Daniel A. Lafontaine*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Cotranscriptional RNA folding is crucial for the timely control of biological processes, but because of its transient nature, its study has remained challenging. While single-molecule Förster resonance energy transfer (smFRET) is unique to investigate transient RNA structures, its application to cotranscriptional studies has been limited to nonnative systems lacking RNA polymerase (RNAP)–dependent features, which are crucial for gene regulation. Here, we present an approach that enables site-specific labeling and smFRET studies of kilobase-length transcripts within native bacterial complexes. By monitoring Escherichia coli nascent riboswitches, we reveal an inverse relationship between elongation speed and metabolite-sensing efficiency and show that pause sites upstream of the translation start codon delimit a sequence hotspot for metabolite sensing during transcription. Furthermore, we demonstrate a crucial role of the bacterial RNAP actively delaying the formation, within the hotspot sequence, of competing structures precluding metabolite binding. Our approach allows the investigation of cotranscriptional regulatory mechanisms in bacterial and eukaryotic elongation complexes.
Original languageEnglish
Article numbere2116155118
Number of pages11
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number45
Early online date5 Nov 2021
Publication statusPublished - 9 Nov 2021


  • Single-molecule FRET
  • Transcription
  • RNA
  • Riboswitch


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