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.
authors: Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.
authors: Kyle E
authors: http://orcid.org/0000-0001-6858-6632
authors: KE
authors: Watters
authors: Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.
authors: Eric J
authors: EJ
authors: Strobel
authors: Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.|Tri-Institutional Training Program in Computational Biology and Medicine at Cornell University, Ithaca, New York, USA; Weill Cornell Medical College, New York, New York, USA; and Memorial Sloan-Kettering Cancer Center, New York, New York, USA.|Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.
authors: Angela M
authors: AM
authors: Yu
authors: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
authors: John T
authors: JT
authors: Lis
authors: Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.|Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA.
authors: Julius B
authors: http://orcid.org/0000-0002-0619-6505
authors: JB
authors: Lucks
mesh_terms: D001409:Bacillus cereus / Q000737:chemistry* / Q000235:genetics; D001483:Base Sequence; D004926:Escherichia coli / Q000737:chemistry* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics; D009154:Mutation; D009690:Nucleic Acid Conformation; D059370:RNA Folding; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D058928:Riboswitch; D018271:Signal Recognition Particle / Q000235:genetics; D061806:Transcription Termination, Genetic; D014158:Transcription, Genetic
chemical_list: D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D058928:Riboswitch; D018271:Signal Recognition Particle