ArticlePLoS genetics2015
Dynamics of Transcription Factor Binding Site Evolution.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it, 103 citations in OpenAlex.
- Conservation and divergence of the p53 gene regulatory network between mice and humans.Oncogene · 2019Pooled it
- Small impact of the host plant physiological state on the genome formula of a nanovirus.PLoS pathogens · 2026Article
- Extensive binding of poorly characterized human transcription factors to genomic dark matter.Nature communications · 2026Article
- Evolutionary Simulations Reveal Role for Genomic Recombination in the Evolution of Gene Regulatory Network Complexity and Robustness.Genome biology and evolution · 2026Article
- 2-Keto-3-deoxy-D-xylonate and 2-oxo-4-hydroxybutyrate as natural and artificial effectors of transcription factors regulating D-xylonate operons in E. coli.Applied microbiology and biotechnology · 2026Article
- Article
- The Constrained Disorder Principle: A Paradigm Shift for Accurate Interactome Mapping and Information Analysis in Complex Biological Systems.Bioengineering (Basel, Switzerland) · 2025Review
- Uncovering the Mechanistic Landscape of Regulatory DNA with Deep Learning.bioRxiv : the preprint server for biology · 2025Article
- CelEst: a unified gene regulatory network for estimating transcription factor activities in C. elegans.Genetics · 2025Article
- Article
- An evaluation of distinct adeno-associated virus vector strategies for driving transgene expression in spinal inhibitory neurons of the rat.Frontiers in neuroscience · 2025Article
- The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR.Nature communications · 2024Article
- Evidence for compensatory evolution within pleiotropic regulatory elements.Genome research · 2024Article
- Identification of transcription factor co-binding patterns with non-negative matrix factorization.Nucleic acids research · 2024Article
- Gene expression networks regulated by human personality.Molecular psychiatry · 2024Review
- High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins.Nucleic acids research · 2023Article
- On the incongruence of genotype-phenotype and fitness landscapes.PLoS computational biology · 2022Article
- Article
- Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana.Genome biology and evolution · 2021Article
- Transcription Factors Drive Opposite Relationships between Gene Age and Tissue Specificity in Male and Female Drosophila Gonads.Molecular biology and evolution · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of "pre-sites" or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.
Indexed as
Identifiers
What OpenQuestion holds
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.