Cotranscriptional folding of a riboswitch at nucleotide resolution
Journal
Nature Structural and Molecular Biology
Journal Volume
23
Journal Issue
12
Pages
1124-1131
Date Issued
2016
Author(s)
Abstract
RNAs 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.
Other Subjects
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, Genetic
Type
journal article