ArticleNature communications2022
Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Chromatin Accessibility Reveals Adaptive Regulatory Variation in a Keystone Freshwater Fish.Molecular ecology · 2026Article
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- Transcriptional regulation of the pneumococcal capsule can dictate serotype-specific infection.Nature communications · 2026Article
- Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.NAR genomics and bioinformatics · 2026Article
- Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.Science advances · 2026Article
- A structure-guided approach to noncoding variant evaluation for transcription factor binding using AlphaFold 3.Nucleic acids research · 2026Article
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- Modulating MyoD1 dosage activates alternate cell fate beyond myogenic differentiation.bioRxiv : the preprint server for biology · 2025Article
- Article
- Transcriptional regulation as a dose-dependent process: insights from transcription factor tuning.Open biology · 2025Review
- Post-translational modification of transcription factors: perspectives in vascular medicine.Cell death & disease · 2025Review
- Genome mining based on transcriptional regulatory networks uncovers a novel locus involved in desferrioxamine biosynthesis.PLoS biology · 2025Article
- Cardiac enhancers: Gateway to the regulatory mechanisms of heart regeneration.Seminars in cell & developmental biology · 2025Review
- Regulation of RNA polymerase II transcription through re-initiation and bursting.Molecular cell · 2025Review
- Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli.Nature communications · 2025Article
- DNA-Protein Binding is Dominated by Short Anchoring Elements.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Nucleotide-level characterization and improvement of l-arabinose- and l-rhamnose-inducible systems in E. coli using a high-throughput approach.Nucleic acids research · 2025Article
- CelEst: a unified gene regulatory network for estimating transcription factor activities in C. elegans.Genetics · 2025Article
- Chromatin enables precise and scalable gene regulation with factors of limited specificity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Binding to binding site clusters has yet to be characterized in depth, and the functional relevance of low-affinity clusters remains uncertain. We characterized transcription factor binding to low-affinity clusters in vitro and found that transcription factors can bind concurrently to overlapping sites, challenging the notion of binding exclusivity. Furthermore, small clusters with binding sites an order of magnitude lower in affinity give rise to high mean occupancies at physiologically-relevant transcription factor concentrations. To assess whether the observed in vitro occupancies translate to transcriptional activation in vivo, we tested low-affinity binding site clusters in a synthetic and native gene regulatory network in S. cerevisiae. In both systems, clusters of low-affinity binding sites generated transcriptional output comparable to single or even multiple consensus sites. This systematic characterization demonstrates that clusters of low-affinity binding sites achieve substantial occupancies, and that this occupancy can drive expression in eukaryotic promoters.
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