ArticleGenetics2012
Why transcription factor binding sites are ten nucleotides long.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 90 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it, 178 citations in OpenAlex.
- Conservation and divergence of the p53 gene regulatory network between mice and humans.Oncogene · 2019Pooled it
- A transcription factor by any other name - function beyond DNA binding and transactivation.EMBO reports · 2026Review
- Emergence Biases in Molecular Evolution.Genome biology and evolution · 2026Review
- The adaptive landscapes of three globaleLife · 2026Article
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.PLoS genetics · 2026Article
- Construction of synthetic protein-binding non-genetic DNA systems in living cells.Nature chemistry · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.bioRxiv : the preprint server for biology · 2026Article
- Predictive modeling of gene expression and localization of DNA binding site using deep convolutional neural networks.PLoS computational biology · 2026Article
- Early feature extraction drives model performance in high-resolution chromatin accessibility prediction.Genome research · 2026Article
- Decoding the role of DNA sequence on protein-DNA co-condensation.PLoS computational biology · 2025Article
- Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites.Nucleic acids research · 2025Article
- PTF-Vāc: An explainable and generative deep co-learning encoder-decoder system for ab initio discovery of plant transcription factor binding sites.Plant communications · 2025Article
- In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences.Nucleic acids research · 2025Article
- Divergence in a eukaryotic transcription factor's co-TF dependence involves multiple intrinsically disordered regions.Nature communications · 2025Article
- Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions.bioRxiv : the preprint server for biology · 2025Article
- Crohn's Disease-associated variant in laccase domain containing 1 (LACC1) modulates T cell gene expression, metabolism and T cell function.Nature communications · 2025Article
- Harnessing p53 for targeted cancer therapy: new advances and future directions.Transcription · 2025Review
- Maize inbreds show allelic variation for diel transcription patterns.bioRxiv : the preprint server for biology · 2024Article
- Generating information-dense promoter sequences with optimal string packing.PLoS computational biology · 2024Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issuedHannenhalli, Sridhar [added]
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Gene expression is controlled primarily by transcription factors, whose DNA binding sites are typically 10 nt long. We develop a population-genetic model to understand how the length and information content of such binding sites evolve. Our analysis is based on an inherent trade-off between specificity, which is greater in long binding sites, and robustness to mutation, which is greater in short binding sites. The evolutionary stable distribution of binding site lengths predicted by the model agrees with the empirical distribution (5-31 nt, with mean 9.9 nt for eukaryotes), and it is remarkably robust to variation in the underlying parameters of population size, mutation rate, number of transcription factor targets, and strength of selection for proper binding and selection against improper binding. In a systematic data set of eukaryotic and prokaryotic transcription factors we also uncover strong relationships between the length of a binding site and its information content per nucleotide, as well as between the number of targets a transcription factor regulates and the information content in its binding sites. Our analysis explains these features as well as the remarkable conservation of binding site characteristics across diverse taxa.
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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.