Thermodynamic and kinetic modeling of transcriptional pausing

doi:10.1073/pnas.0600508103

Thermodynamic and kinetic modeling of transcriptional pausing

*BioMaPS Institute for Quantitative Biology,
^‡Department of Physics and Astronomy,
^¶Department of Chemistry and Chemical Biology, and
^‖Howard Hughes Medical Institute and Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ 08854; and
^§Department of Biochemistry, New York University Medical Center, New York, NY 10016

Communicated by Peter H. von Hippel, University of Oregon, Eugene, OR, January 20, 2006
↵ ^†V.R.T. and D.ÓM. contributed equally to this work. (received for review September 10, 2005)

Abstract

We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA–DNA, DNA–RNA, and RNA–RNA base pairing associated with (i) the translocational and size fluctuations of the transcription bubble; (ii) changes in the associated DNA–RNA hybrid; and (iii) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotranscriptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process.

Footnotes

**To whom the correspondence should be addressed. E-mail: andreir{at}physics.rutgers.edu
Author contributions: V.R.T., D.ÓM., A.M.S., R.H.E., E.N., and A.E.R. designed research; V.R.T., D.ÓM., A.M.S., V.E., E.N., and A.E.R. performed research; V.R.T., D.ÓM., and A.E.R. analyzed data; and V.R.T., D.ÓM., R.H.E., and A.E.R. wrote the paper.
Conflict of interest statement: No conflicts declared.
Abbreviations:

EC,

elongation complex;

MBF,

multiple bubbles with RNA folding;

MBNF,

multiple bubbles without RNA folding;

NTP,

nucleoside triphosphate;

PPV,

positive predictive value;

RNAP,

RNA polymerase;

SBF,

single bubble with RNA folding;

SBNF,

single bubble without RNA folding;

TP,

true positives.