ArticlePhysical biology2014
Comparison of the theoretical and real-world evolutionary potential of a genetic circuit.
Article in Physical biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Article
- Motivational interviewing for genetic counseling: A unified framework for persuasive and equipoise conversations.Journal of genetic counseling · 2022Article
- Predictive shifts in free energy couple mutations to their phenotypic consequences.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression.Annual review of biophysics · 2019Review
- Connecting single-cell properties to collective behavior in multiple wild isolates of the Enterobacter cloacae complex.PloS one · 2019Article
- Effective models and the search for quantitative principles in microbial evolution.Current opinion in microbiology · 2018Review
- Self-consistent theory of transcriptional control in complex regulatory architectures.PloS one · 2017Article
- Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP.Scientific reports · 2016Article
- Sort-seq under the hood: implications of design choices on large-scale characterization of sequence-function relations.BMC genomics · 2016Article
- Predicting the impact of promoter variability on regulatory outputs.Scientific reports · 2015Article
- Dynamics of Transcription Factor Binding Site Evolution.PLoS genetics · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
With the development of next-generation sequencing technologies, many large scale experimental efforts aim to map genotypic variability among individuals. This natural variability in populations fuels many fundamental biological processes, ranging from evolutionary adaptation and speciation to the spread of genetic diseases and drug resistance. An interesting and important component of this variability is present within the regulatory regions of genes. As these regions evolve, accumulated mutations lead to modulation of gene expression, which may have consequences for the phenotype. A simple model system where the link between genetic variability, gene regulation and function can be studied in detail is missing. In this article we develop a model to explore how the sequence of the wild-type lac promoter dictates the fold-change in gene expression. The model combines single-base pair resolution maps of transcription factor and RNA polymerase binding energies with a comprehensive thermodynamic model of gene regulation. The model was validated by predicting and then measuring the variability of lac operon regulation in a collection of natural isolates. We then implement the model to analyze the sensitivity of the promoter sequence to the regulatory output, and predict the potential for regulation to evolve due to point mutations in the promoter region.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.