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Versatility of Cooperative Transcriptional Activation: A Thermodynamical Modeling Analysis for Greater-Than-Additive and Less-Than-Additive Effects

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Foxa2 and Nurr1 Synergistically Yield A9 Nigral Dopamine Neurons Exhibiting Improved Differentiation, Function, and Cell Survival
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Transcription Activation by the Escherichia coli Cyclic AMP
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Coupled energetics of λ cro repressor self-assembly and site-specific DNA operator binding II: cooperative interactions of cro dimers
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Nonlinear fokker-planck equations : fundamentals and applications
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When Activators Repress and Repressors Activate: A Qualitative Analysis of the Shea–Ackers Model
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The OR control system of bacteriophage lambda
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Promoter recognition by Escherichia coli RNA polymerase
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Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics
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Computational Models for Neurogenic Gene Expression in the Drosophila Embryo
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Transcriptional Enhancers in Animal Development and Evolution
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Transcriptional regulation by the numbers: applications
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Transcriptional regulation by the numbers: models
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Nurr1 is phosphorylated by ERK2 in vitro and its phosphorylation upregulates tyrosine hydroxylase expression in SH-SY5Y cells
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Stability analysis of stationary states of mean field models described by Fokker–Planck equations
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Promoter recognition by Escherichia coli RNA polymerase. Effects of substitutions in the spacer DNA separating the -10 and -35 regions.
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The Enhanceosome and Transcriptional Synergy
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Promoter recognition by Escherichia coli RNA polymerase: effects of base substitutions in the -10 and -35 regions
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λ Repressor and cro—components of an efficient molecular switch
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Transcriptional activation by recruitment
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Environment‐specific combinatorial cis‐regulation in synthetic promoters
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Analysis of combinatorial cis-regulation in synthetic and genomic promoters
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Combinatorial transcriptional control of the lactose operon of Escherichia coli
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Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
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Quantitative dissection of the simple repression input–output function
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Quantitative model for gene regulation by lambda phage repressor.
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Synergistic activation of transcription by Escherichia coli cAMP receptor protein.
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Binding affinity of Escherichia coli RNA polymerasemiddle dotsigma54 holoenzyme for the glnAp2, nifH and nifL promoters
inferredcites →https://doi.org/10.1101/gad.10.20.2540openalex-snapshot
Assembly of the isomerized TFIIA--TFIID--TATA ternary complex is necessary and sufficient for gene activation.
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Reentrant transition induced by multiplicative noise in the time-dependent Ginzburg-Landau model
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First-order nonequilibrium phase transition in a spatially extended system
inferredcites →https://doi.org/10.1103/physreve.57.r2495openalex-snapshot
Nonequilibrium transitions induced by multiplicative noise
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Noise-Induced Nonequilibrium Phase Transition
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Genetic networks controlling the development of midbrain dopaminergic neurons
inferredcites →https://doi.org/10.1126/science.8091212openalex-snapshot
Synergistic Activation of Transcription by Bacteriophage λ cI Protein and E. coli cAMP Receptor Protein
inferredcites →https://doi.org/10.1126/scisignal.2002077openalex-snapshot
The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity
inferredcites →https://doi.org/10.1128/jvi.66.8.4803-4813.1992openalex-snapshot
Transcriptional synergy by the Epstein-Barr virus transactivator ZEBRA
inferredcites →https://doi.org/10.1128/jvi.68.11.7628-7633.1994openalex-snapshot
Activation of the Epstein-Barr virus BMRF1 and BZLF1 promoters by ZEBRA in Saccharomyces cerevisiae
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Transcriptional Control in Drosophila
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An Introduction to Systems Biology
inferredcites →https://doi.org/10.1242/dev.126.18.4017openalex-snapshot
Nurr1, an orphan nuclear receptor, is a transcriptional activator of endogenous tyrosine hydroxylase in neural progenitor cells derived from the adult brain
inferredcites →https://doi.org/10.1371/journal.pbio.0050325openalex-snapshot
The foxa2 Gene Controls the Birth and Spontaneous Degeneration of Dopamine Neurons in Old Age
inferredcites →https://doi.org/10.1371/journal.pcbi.0030084openalex-snapshot
Enhancer Responses to Similarly Distributed Antagonistic Gradients in Development
inferredcites →https://doi.org/10.1371/journal.pcbi.1000935openalex-snapshot
Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression
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Quantitative analysis of the ternary complex of RNA polymerase, cyclic AMP receptor protein and DNA by fluorescence anisotropy measurements.
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Mathematical modeling of gene expression: a guide for the perplexed biologist

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Transcriptional Kinetic Synergy: A Complex Landscape Revealed by Integrating Modelling and Synthetic Biology
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Non-linear Dynamics in Transcriptional Regulation: Biological Logic Gates
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Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate
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Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle
inferred← citeshttps://doi.org/10.1016/j.cels.2023.02.003openalex-snapshot
Transcriptional kinetic synergy: A complex landscape revealed by integrating modeling and synthetic biology
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Three-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data
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Integrating regulatory information via combinatorial control of the transcription cycle
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RNA POLYMERASE ON DNA AS A FERMI SYSTEM: INTERNAL ENERGY, ENTROPY, HEAT CAPACITY, AND NEGATIVE TEMPERATURE
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Gene Regulation in and out of Equilibrium
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Effective Single-Step Posttranscriptional Dynamics Allowing for a Direct Maximum Likelihood Estimation of Transcriptional Activity and the Quantification of Sources of Gene Expression Variability with an Illustration for the Hypoxia and TNFαRegulated Inflammatory Pathway
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Analysis of the transcriptional logic governing differential spatial expression in Hh target genes
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Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies
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Crosstalk and Signaling Switches in Mitogen-Activated Protein Kinase Cascades
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Thermodynamic Modelling of Transcriptional Control: A Sensitivity Analysis
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