Cotranscriptional folding of a riboswitch at nucleotide resolution Journal Article

Authors: Watters, K. E.; Strobel, E. J.; Yu, A. M.; Lis, J. T.; Lucks, J. B.
Article Title: Cotranscriptional folding of a riboswitch at nucleotide resolution
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.
Keywords: kinetics; transcription; recognition; in-vitro; dynamics; shape; elongation; coli rna-polymerase; fluoride; tpp riboswitch
Journal Title: Nature Structural & Molecular Biology
Volume: 23
Issue: 12
ISSN: 1545-9985
Publisher: Nature Publishing Group  
Date Published: 2016-12-01
Start Page: 1124
End Page: 1131
Language: English
ACCESSION: WOS:000389559300015
DOI: 10.1038/nsmb.3316
PUBMED: 27798597
PMCID: PMC5497173
Notes: Article -- Source: Wos
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  1. Angela M Yu
    2 Yu