ArticleNucleic acids research2007
General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 53 citations in OpenAlex.
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- Cooperative kinetics of ligand binding to linear polymers.Computational and structural biotechnology journal · 2022Article
- Effects of size, cooperativity, and competitive binding on protein positioning on DNA.Biophysical journal · 2021Article
- A Predictive Model of Antibody Binding in the Presence of IgG-Interacting Bacterial Surface Proteins.Frontiers in immunology · 2021Article
- An Overview of Emergent Order in Far-from-Equilibrium Driven Systems: From Kuramoto Oscillators to Rayleigh-Bénard Convection.Entropy (Basel, Switzerland) · 2020Article
- DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?Computational and structural biotechnology journal · 2019Review
- Article
- Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.Nucleic acids research · 2014Article
- Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development.Genome research · 2014Article
- Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.PLoS computational biology · 2014Article
- A lattice model for transcription factor access to nucleosomal DNA.Biophysical journal · 2010Article
- Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression.PLoS computational biology · 2010Article
- Predicting gene-regulation functions: lessons from temperate bacteriophages.Biophysical journal · 2010Article
- A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.PloS one · 2009Article
- An ensemble model of competitive multi-factor binding of the genome.Genome research · 2009Article
- Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities.Nucleic acids research · 2009Article
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1 author at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The transfer matrix methodology is proposed as a systematic tool for the statistical-mechanical description of DNA-protein-drug binding involved in gene regulation. We show that a genetic system of several cis-regulatory modules is calculable using this method, considering explicitly the site-overlapping, competitive, cooperative binding of regulatory proteins, their multilayer assembly and DNA looping. In the methodological section, the matrix models are solved for the basic types of short- and long-range interactions between DNA-bound proteins, drugs and nucleosomes. We apply the matrix method to gene regulation at the O(R) operator of phage lambda. The transfer matrix formalism allowed the description of the lambda-switch at a single-nucleotide resolution, taking into account the effects of a range of inter-protein distances. Our calculations confirm previously established roles of the contact CI-Cro-RNAP interactions. Concerning long-range interactions, we show that while the DNA loop between the O(R) and O(L) operators is important at the lysogenic CI concentrations, the interference between the adjacent promoters P(R) and P(RM) becomes more important at small CI concentrations. A large change in the expression pattern may arise in this regime due to anticooperative interactions between DNA-bound RNA polymerases. The applicability of the matrix method to more complex systems is discussed.
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