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

Zamft B,Bintu L,Ishibashi T,Bustamante C

doi

10.1073/pnas.1205063109

subject

Has Abstract

pub_date

2012-06-05 00:00:00

pages

8948-53

issue

23

eissn

0027-8424

issn

1091-6490

pii

1205063109

journal_volume

109

pub_type

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