ArticlePloS one2012
Cooperative binding of transcription factors promotes bimodal gene expression response.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Modeling of gene regulatory networks: an annotated glossary.Trends in plant science · 2026Review
- RNA G-quadruplexes mediate cooperativity in HNRNPH binding and splicing regulation.bioRxiv : the preprint server for biology · 2026Article
- Loss of YTHDF2 enhances Th9 programming and CAR-Th9 cell antitumor efficacy.Nature immunology · 2025Article
- Simplifications and approximations in a single-gene circuit modeling.Scientific reports · 2024Article
- BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites.Genome biology · 2024Article
- Evolutionary innovation through transcription factor rewiring in microbes is shaped by levels of transcription factor activity, expression, and existing connectivity.PLoS biology · 2023Article
- Multifaceted Transcriptional Network of Estrogen-Related Receptor Alpha in Health and Disease.International journal of molecular sciences · 2023Review
- Concentration-dependent transcriptional switching through a collective action of cis-elements.Science advances · 2022Article
- Computational identification of new potential transcriptional partners of ERRα in breast cancer cells: specific partners for specific targets.Scientific reports · 2022Article
- Liquid-Liquid Phase Separation in Chromatin.Cold Spring Harbor perspectives in biology · 2022Review
- Efficient Framework Analysis for Targeted Drug Delivery Based on Internet of Bio-NanoThings.Arabian journal for science and engineering · 2021Article
- Decoupled molecules with binding polynomials of bidegree (n, 2).Journal of mathematical biology · 2019Article
- Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization.PloS one · 2018Article
- Characterization of noise in multistable genetic circuits reveals ways to modulate heterogeneity.PloS one · 2018Article
- Gene switching rate determines response to extrinsic perturbations in the self-activation transcriptional network motif.Scientific reports · 2016Article
- Cooperative binding: a multiple personality.Journal of mathematical biology · 2016Article
- Promoters Architecture-Based Mechanism for Noise-Induced Oscillations in a Single-Gene Circuit.PloS one · 2016Article
- Cooperativity to increase Turing pattern space for synthetic biology.ACS synthetic biology · 2015Article
- Noise and information transmission in promoters with multiple internal States.Biophysical journal · 2014Article
- Modeling stochastic noise in gene regulatory systems.Quantitative biology (Beijing, China) · 2014Article
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3 authors.
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Abstract
In the present work we extend and analyze the scope of our recently proposed stochastic model for transcriptional regulation, which considers an arbitrarily complex cis-regulatory system using only elementary reactions. Previously, we determined the role of cooperativity on the intrinsic fluctuations of gene expression for activating transcriptional switches, by means of master equation formalism and computer simulation. This model allowed us to distinguish between two cooperative binding mechanisms and, even though the mean expression levels were not affected differently by the acting mechanism, we showed that the associated fluctuations were different. In the present generalized model we include other regulatory functions in addition to those associated to an activator switch. Namely, we introduce repressive regulatory functions and two theoretical mechanisms that account for the biphasic response that some cis-regulatory systems show to the transcription factor concentration. We have also extended our previous master equation formalism in order to include protein production by stochastic translation of mRNA. Furthermore, we examine the graded/binary scenarios in the context of the interaction energy between transcription factors. In this sense, this is the first report to show that the cooperative binding of transcription factors to DNA promotes the "all-or-none" phenomenon observed in eukaryotic systems. In addition, we confirm that gene expression fluctuation levels associated with one of two cooperative binding mechanism never exceed the fluctuation levels of the other.
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