Sequence-Resolved Detection of Pausing by Single RNA Polymerase Molecules

Herbert, Kristina M.; Porta, A. La; Wong, Becky J.; Mooney, Rachel A.; Neuman, Keir C.; Landick, Robert; Block, Steven M.

doi:10.1016/j.cell.2006.04.032

Cited by 258 publications

(424 citation statements)

References 47 publications

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“…Events in elongation, e.g. pauses [31], could contribute to the variance of elongation times. High variance in elongation times would introduce correlations between consecutive intervals.…”

Section: Resultsmentioning

confidence: 99%

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara‐1 promoter

et al. 2012

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a b s t r a c tThe kinetics of transcription initiation in Escherichia coli depend on the duration of two rate-limiting steps, the closed and the open complex formation. In a lac promoter variant, P lac/ara-1 , the kinetics of these steps is controlled by IPTG and arabinose. From in vivo single-RNA measurements, we find that induction affects the mean and normalized variance of the intervals between consecutive RNA productions. Transcript production is sub-Poissonian in all conditions tested. The kinetics of each step is independently controlled by a different inducer. We conclude that the regulatory mechanism of P lac/ara-1 allows the stochasticity of gene expression to be environment-dependent.

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“…Events in elongation, e.g. pauses [31], could contribute to the variance of elongation times. High variance in elongation times would introduce correlations between consecutive intervals.…”

Section: Resultsmentioning

confidence: 99%

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara‐1 promoter

et al. 2012

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“…These rates are further slowed by transcriptional pausing to regulate arrest and termination 5,6,7 by ∼seconds per pause. Even "fast" processes such as bacteriophage DNA ejection have translocation times greater than 10µs/bp 8,9 .…”

Section: Introductionmentioning

confidence: 99%

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

Morriss-Andrews

Rottler

Plotkin

2010

The Journal of Chemical Physics

117

165

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We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with minimal phenomenology. Persistence length, degree of stacking, and twist are studied by molecular dynamics simulation as functions of temperature, salt concentration, sequence, interaction potential strength, and local position along the chain, for both single-and double-stranded DNA where appropriate. The model of DNA shows several phase transitions and crossover regimes in addition to dehybridization, including unstacking, untwisting, and collapse which affect mechanical properties such as rigidity and persistence length. The model also exhibits chirality with a stable right-handed and metastable left-handed helix.

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“…This approximation assumes that the elongation time is negligible, which relies on observation that the durations of the closed and the open complex formations (in the order of 10 3 s) [1,2,13,20] are much longer than elongation (in the order of 10 1 or 10 2 s) [21,22]. Moreover, in prokaryotes, translation is coupled to transcription [23], and can initiate as soon as the ribosome binding site region (RBS) of the RNA is formed (Shine-Dalgarno sequence) [24].…”

Section: Methodsmentioning

confidence: 99%

Effects of multimerization on the temporal variability of protein complex abundance

et al. 2013

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We explore whether the process of multimerization can be used as a means to regulate noise in the abundance of functional protein complexes. Additionally, we analyze how this process affects the mean level of these functional units, response time of a gene, and temporal correlation between the numbers of expressed proteins and of the functional multimers. We show that, although multimerization increases noise by reducing the mean number of functional complexes it can reduce noise in comparison with a monomer, when abundance of the functional proteins are comparable. Alternatively, reduction in noise occurs if both monomeric and multimeric forms of the protein are functional. Moreover, we find that multimerization either increases the response time to external signals or decreases the correlation between number of functional complexes and protein production kinetics. Finally, we show that the results are in agreement with recent genome-wide assessments of cell-to-cell variability in protein numbers and of multimerization in essential and non-essential genes in Escherichia coli, and that the effects of multimerization are tangible at the level of genetic circuits.

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Sequence-Resolved Detection of Pausing by Single RNA Polymerase Molecules

Cited by 258 publications

References 47 publications

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara‐1 promoter

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara‐1 promoter

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

Effects of multimerization on the temporal variability of protein complex abundance

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