title: Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases.
abstract: RNA polymerase pausing represents an important mechanism of transcriptional regulation. In this study, we use a single-molecule transcription assay to investigate the effect of template base-pair composition on pausing by RNA polymerase II and the evolutionarily distinct mitochondrial polymerase Rpo41. For both enzymes, pauses are shorter and less frequent on GC-rich templates. Significantly, incubation with RNase abolishes the template dependence of pausing. A kinetic model, wherein the secondary structure of the nascent RNA poses an energetic barrier to pausing by impeding backtracking along the template, quantitatively predicts the pause densities and durations observed. The energy barriers extracted from the data correlate well with RNA folding energies obtained from cotranscriptional folding simulations. These results reveal that RNA secondary structures provide a cis-acting mechanism by which sequence modulates transcriptional elongation.
authors.affiliation: Jason L. Choy Laboratory of Single-Molecule Biophysics and Department of Physics, University of California, Berkeley, CA 94720, USA.
authors.forename: Bradley
authors.initials: B
authors.lastname: Zamft
authors.forename: Lacramioara
authors.initials: L
authors.lastname: Bintu
authors.forename: Toyotaka
authors.initials: T
authors.lastname: Ishibashi
authors.forename: Carlos
authors.initials: C
authors.lastname: Bustamante
mesh_terms: D001482:Base Composition; D003198:Computer Simulation; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D024101:Mitochondrial Proteins / Q000235:genetics*; D008954:Models, Biological; D016941:Myxococcus xanthus / Q000235:genetics; D009841:Oligonucleotides / Q000235:genetics; D016133:Polymerase Chain Reaction; D012313:RNA / Q000235:genetics*; D059370:RNA Folding / Q000235:genetics; D012319:RNA Polymerase II / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000502:physiology; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology*
chemical_list: D024101:Mitochondrial Proteins; D009841:Oligonucleotides; D029701:Saccharomyces cerevisiae Proteins; D012313:RNA; D012319:RNA Polymerase II; D012321:DNA-Directed RNA Polymerases; C487996:RPO41 protein, S cerevisiae