ArticlePLoS biology2010
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.
Article in PLoS biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
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
129 citing papers in PubMed, 204 citations in OpenAlex.
- Retracing and rewriting the evolutionary trajectories of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- Motif-based models accurately predict cell type-specific distal regulatory elements.Nature communications · 2025Article
- MicroRNA-mediated network redundancy is constrained by purifying selection and contributes to expression robustness in Drosophila melanogaster.Communications biology · 2024Article
- Repeated Shifts in Sociality Are Associated With Fine-tuning of Highly Conserved and Lineage-Specific Enhancers in a Socially Flexible Bee.Molecular biology and evolution · 2024Article
- Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro.Nature communications · 2024Article
- Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions.Journal of molecular evolution · 2024Article
- Understanding species-specific and conserved RNA-protein interactionsbioRxiv : the preprint server for biology · 2024Article
- Position-specific evolution in transcription factor binding sites, and a fast likelihood calculation for the F81 model.Royal Society open science · 2024Article
- Widespread transposon co-option in theScience advances · 2022Article
- Evolution of transcription factor binding through sequence variations and turnover of binding sites.Genome research · 2022Article
- Disparate Dynamics of Gene Body andPlants (Basel, Switzerland) · 2021Article
- Rapid Evolution of Autosomal Binding Sites of the Dosage Compensation Complex inFrontiers in genetics · 2021Article
- Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos.eLife · 2020Article
- Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data.Molecular biology and evolution · 2020Article
- Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays.Nucleic acids research · 2020Article
- Arginine Deiminase and Biotin Metabolism Signaling Pathways Play an Important Role in Human-Derived Serotype V, ST1 Streptococcus agalactiae Virulent Strain upon Infected Tilapia.Animals : an open access journal from MDPI · 2020Article
- Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes.BMC evolutionary biology · 2019Article
- Promoter conservation in HDACs points to functional implications.BMC genomics · 2019Article
- The Role of Chromatin Accessibility in cis-Regulatory Evolution.Genome biology and evolution · 2019Article
- ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in theGenome research · 2019Article
69 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
Changes in gene expression play an important role in evolution, yet the molecular mechanisms underlying regulatory evolution are poorly understood. Here we compare genome-wide binding of the six transcription factors that initiate segmentation along the anterior-posterior axis in embryos of two closely related species: Drosophila melanogaster and Drosophila yakuba. Where we observe binding by a factor in one species, we almost always observe binding by that factor to the orthologous sequence in the other species. Levels of binding, however, vary considerably. The magnitude and direction of the interspecies differences in binding levels of all six factors are strongly correlated, suggesting a role for chromatin or other factor-independent forces in mediating the divergence of transcription factor binding. Nonetheless, factor-specific quantitative variation in binding is common, and we show that it is driven to a large extent by the gain and loss of cognate recognition sequences for the given factor. We find only a weak correlation between binding variation and regulatory function. These data provide the first genome-wide picture of how modest levels of sequence divergence between highly morphologically similar species affect a system of coordinately acting transcription factors during animal development, and highlight the dominant role of quantitative variation in transcription factor binding over short evolutionary distances.
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.