ArticleNucleic acids research2021
A balancing act in transcription regulation by response regulators: titration of transcription factor activity by decoy DNA binding sites.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 25 citations in OpenAlex.
- Construction of synthetic protein-binding non-genetic DNA systems in living cells.Nature chemistry · 2026Article
- Transcriptional condensates encode a "golden mean" to optimize enhancer-promoter communication across genomic distances.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Escherichia coli replication initiator DnaA is titrated on the chromosome.Nature communications · 2025Article
- Article
- Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.Plant & cell physiology · 2025Review
- Sequestration of gene products by decoys enhances precision in the timing of intracellular events.Scientific reports · 2024Article
- Pervasive under-dominance in gene expression underlying emergent growth trajectories in Arabidopsis thaliana hybrids.Genome biology · 2023Article
- Exploring the mono-/bistability range of positively autoregulated signaling systems in the presence of competing transcription factor binding sites.PLoS computational biology · 2022Article
- High Abundance of Transcription Regulators Compacts the Nucleoid in Escherichia coli.Journal of bacteriology · 2022Article
- Article
- Prognostic and immune correlation evaluation of a novel cuproptosis-related genes signature in hepatocellular carcinoma.Frontiers in pharmacology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Studies of transcription regulation are often focused on binding of transcription factors (TFs) to a small number of promoters of interest. It is often assumed that TFs are in great excess to their binding sites (TFBSs) and competition for TFs between DNA sites is seldom considered. With increasing evidence that TFBSs are exceedingly abundant for many TFs and significant variations in TF and TFBS numbers occur during growth, the interplay between a TF and all TFBSs should not be ignored. Here, we use additional decoy DNA sites to quantitatively analyze how the relative abundance of a TF to its TFBSs impacts the steady-state level and onset time of gene expression for the auto-activated Escherichia coli PhoB response regulator. We show that increasing numbers of decoy sites progressively delayed transcription activation and lowered promoter activities. Perturbation of transcription regulation by additional TFBSs did not require extreme numbers of decoys, suggesting that PhoB is approximately at capacity for its DNA sites. Addition of decoys also converted a graded response to a bi-modal response. We developed a binding competition model that captures the major features of experimental observations, providing a quantitative framework to assess how variations in TFs and TFBSs influence transcriptional responses.
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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.