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Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates

74 Pages Posted: 18 Mar 2020 Sneak Peek Status: Review Complete

See all articles by Tomasz W. Turowski

Tomasz W. Turowski

University of Edinburgh - Wellcome Centre for Cell Biology

Elisabeth Petfalski

University of Edinburgh - Wellcome Centre for Cell Biology

Benjamin D. Goddard

University of Edinburgh

Sarah L. French

University of Virginia - Department of Microbiology, Immunology and Cancer Biology

Aleksandra Helwak

University of Edinburgh - Wellcome Centre for Cell Biology

David Tollervey

University of Edinburgh - Wellcome Centre for Cell Biology

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Abstract

Transcription elongation rates are important for RNA processing, but sequence-specific regulation is poorly understood. We addressed this in vivo, analyzing RNAPI in S.cerevisiae. Analysis of Miller chromatin spreads and mapping RNAPI using UV crosslinking, revealed a marked 5' bias and strikingly uneven local polymerase occupancy, indicating substantial variation in transcription speed. Two features of the nascent transcript correlated with RNAPI distribution; folding energy and G+C-content. In vitro experiments confirmed that strong RNA structures close to the polymerase promote forward translocation and limit backtracking, whereas high G+C within the transcription bubble slows elongation. We developed a mathematical model for RNAPI elongation, which confirmed the importance of nascent RNA folding in transcription. RNAPI from S.pombe was similarly sensitive to transcript folding, as were S.cerevisiae RNAPII and RNAPIII. For RNAPII, unstructured RNA, which favors slowed elongation, was associated with faster cotranscriptional splicing and proximal splice site usage indicating regulatory significance for transcript folding.

Keywords: Transcription elongation, RNA polymerase 1, RNA folding, yeast, mathematical modeling, rDNA, cotranscriptional events, RNA processing

Suggested Citation

Turowski, Tomasz W. and Petfalski, Elisabeth and Goddard, Benjamin D. and French, Sarah L. and Helwak, Aleksandra and Tollervey, David, Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates. Available at SSRN: https://ssrn.com/abstract=3551619 or http://dx.doi.org/10.2139/ssrn.3551619
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Tomasz W. Turowski

University of Edinburgh - Wellcome Centre for Cell Biology

United Kingdom

Elisabeth Petfalski

University of Edinburgh - Wellcome Centre for Cell Biology

United Kingdom

Benjamin D. Goddard

University of Edinburgh

Old College
South Bridge
Edinburgh, Scotland EH8 9JY
United Kingdom

Sarah L. French

University of Virginia - Department of Microbiology, Immunology and Cancer Biology

1400 University Ave
Charlottesville, VA 22903
United States

Aleksandra Helwak

University of Edinburgh - Wellcome Centre for Cell Biology

United Kingdom

David Tollervey (Contact Author)

University of Edinburgh - Wellcome Centre for Cell Biology ( email )

United Kingdom

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