Watters K.EStrobel E.JANGELA YU-CHEN LINLis J.TLucks J.B.2022-11-162022-11-16201615459993https://www.scopus.com/inward/record.uri?eid=2-s2.0-84992755504&doi=10.1038%2fnsmb.3316&partnerID=40&md5=1c1eef1a34db390630545872f7dd033chttps://scholars.lib.ntu.edu.tw/handle/123456789/625571RNAs can begin to fold immediately as they emerge from RNA polymerase. During cotranscriptional folding, interactions between nascent RNAs and ligands are able to direct the formation of alternative RNA structures, a feature exploited by noncoding RNAs called riboswitches to make gene-regulatory decisions. Despite their importance, cotranscriptional folding pathways have yet to be uncovered with sufficient resolution to reveal how cotranscriptional folding governs RNA structure and function. To access cotranscriptional folding at nucleotide resolution, we extended selective 2′-hydroxyl acylation analyzed by primer-extension sequencing (SHAPE-seq) to measure structural information of nascent RNAs during transcription. Using cotranscriptional SHAPE-seq, we determined how the cotranscriptional folding pathway of the Bacillus cereus crcB fluoride riboswitch undergoes a ligand-dependent bifurcation that delays or promotes terminator formation via a series of coordinated structural transitions. Our results directly link cotranscriptional RNA folding to a genetic decision and establish a framework for cotranscriptional analysis of RNA structure at nucleotide resolution.bacterial RNA; fluoride; nucleotide; signal recognition particle; bacterial RNA; Escherichia coli protein; riboswitch; acylation; Article; Bacillus cereus; comparative study; controlled study; Escherichia coli; gene function; in vitro study; next generation sequencing; nonhuman; priority journal; ribosome; riboswitch; RNA folding; RNA sequence; RNA structure; RNA transcription; transcription regulation; chemistry; conformation; genetic transcription; genetics; mutation; nucleotide sequence; transcription termination; Bacillus cereus; Base Sequence; Escherichia coli; Escherichia coli Proteins; Mutation; Nucleic Acid Conformation; Riboswitch; RNA Folding; RNA, Bacterial; Signal Recognition Particle; Transcription Termination, Genetic; Transcription, Geneticjournal article10.1038/nsmb.3316277985972-s2.0-84992755504