Detecting sequence dependent transcriptional pauses from RNA and protein number time series

Frank Emmert-Streib,Antti Häkkinen,Andre S Ribeiro

doi:10.1186/1471-2105-13-152

Frank Emmert-Streib, Antti Häkkinen + Show 1 more

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https://doi.org/10.1186/1471-2105-13-152

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Abstract

BackgroundEvidence suggests that in prokaryotes sequence-dependent transcriptional pauses affect the dynamics of transcription and translation, as well as of small genetic circuits. So far, a few pause-prone sequences have been identified from in vitro measurements of transcription elongation kinetics.ResultsUsing a stochastic model of gene expression at the nucleotide and codon levels with realistic parameter values, we investigate three different but related questions and present statistical methods for their analysis. First, we show that information from in vivo RNA and protein temporal numbers is sufficient to discriminate between models with and without a pause site in their coding sequence. Second, we demonstrate that it is possible to separate a large variety of models from each other with pauses of various durations and locations in the template by means of a hierarchical clustering and a random forest classifier. Third, we introduce an approximate likelihood function that allows to estimate the location of a pause site.ConclusionsThis method can aid in detecting unknown pause-prone sequences from temporal measurements of RNA and protein numbers at a genome-wide scale and thus elucidate possible roles that these sequences play in the dynamics of genetic networks and phenotype.

Highlights

Evidence suggests that in prokaryotes sequence-dependent transcriptional pauses affect the dynamics of transcription and translation, as well as of small genetic circuits
The long-pause site is at nucleotide 500 and has the same kinetic properties as a his pause, i.e., the efficiency of pausing is εnp = 0.8 and the mean duration is τnp = 47 s [5]
So far the identification of pause-prone sequences has relied on in vitro studies that make use of complex measurement procedures to characterize the kinetics of elongation of the RNA polymerase (RNAP) [4,6,7,53]

Summary

Introduction

Evidence suggests that in prokaryotes sequence-dependent transcriptional pauses affect the dynamics of transcription and translation, as well as of small genetic circuits. One mechanism that likely contributes to transcriptional noise in prokaryotes is RNA polymerase (RNAP) pausing during elongation [1,2]. Pausing enhances the propensity for collisions between consecutive RNAPs in the template [3] and, in some cases, of premature terminations [4], when hairpin loops form in the transcript, facilitating the recruitment of Rho-factor, a protein that dissociates the RNA from the DNA template and RNA polymerase [5]. The distance of the hairpin from the RNA 3 end and the RNA sequence affect pause duration and proneness for premature termination [4], indicating that the kinetics of this process is sequence dependent [6].

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