The mechanism of variability in transcription start site selection

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Abstract

During transcription initiation, RNA polymerase (RNAP) binds to promoter DNA, unwinds promoter DNA to form an RNAP-promoter open complex (RPo) containing a single-stranded 'transcription bubble,' and selects a transcription start site (TSS). TSS selection occurs at different positions within the promoter region, depending on promoter sequence and initiating-substrate concentration. Variability in TSS selection has been proposed to involve DNA 'scrunching' and 'anti-scrunching,' the hallmarks of which are: (i) forward and reverse movement of the RNAP leading edge, but not trailing edge, relative to DNA, and (ii) expansion and contraction of the transcription bubble. Here, using in vitro and in vivo protein-DNA photocrosslinking and single-molecule nanomanipulation, we show bacterial TSS selection exhibits both hallmarks of scrunching and anti-scrunching, and we define energetics of scrunching and anti-scrunching. The results establish the mechanism of TSS selection by bacterial RNAP and suggest a general mechanism for TSS selection by bacterial, archaeal, and eukaryotic RNAP.

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Libing Yu

Department of Chemistry, Rutgers University, Piscataway, United States

Competing interests
The authors declare that no competing interests exist.
Jared Winkelman

Department of Chemistry, Rutgers University, Piscataway, United States

Competing interests
The authors declare that no competing interests exist.
Chirangini Pukhrambam

Department of Genetics, Rutgers University, Piscataway, United States

Competing interests
The authors declare that no competing interests exist.
Terence Strick

Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, Paris, France

Competing interests
The authors declare that no competing interests exist.
Bryce E Nickels

Department of Genetics, Rutgers University, Piscataway, United States

For correspondence
bnickels@waksman.rutgers.edu

Competing interests
The authors declare that no competing interests exist.
Richard H Ebright

Department of Chemistry, Rutgers University, Piscataway, United States

For correspondence
ebright@waksman.rutgers.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8915-7140

Funding

National Institutes of Health (GM041376)

Richard H Ebright

National Institutes of Health (GM118059)

Bryce E Nickels

European Science Foundation (EURYI)

Terence Strick

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.