ArticlePLoS computational biology2006
Large-scale turnover of functional transcription factor binding sites in Drosophila.
Article in PLoS computational biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 145 papers.
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Who cites it
145 citing papers in PubMed.
- Article
- Retracing and rewriting the evolutionary trajectories of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary turnover of key amino acids explains conservation of function without conservation of sequence in transcriptional activation domains.PLoS genetics · 2026Article
- Position-specific evolution in transcription factor binding sites, and a fast likelihood calculation for the F81 model.Royal Society open science · 2024Article
- Polycomb Recruiters Inside and Outside of the Repressed Domains.International journal of molecular sciences · 2023Review
- Transcription factor binding sites are frequently under accelerated evolution in primates.Nature communications · 2023Article
- Recruitment to Chromatin of (GA)n-Associated Factors GAF and Psq in the Transgenic Model System Depends on the Presence of Architectural Protein Binding Sites.Doklady. Biochemistry and biophysics · 2022Article
- PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information.Bioinformatics (Oxford, England) · 2022Article
- Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap-, Zeste-, Psq-, and Adf1-associated proteins.Cellular and molecular life sciences : CMLS · 2022Article
- Evolution of transcription factor binding through sequence variations and turnover of binding sites.Genome research · 2022Article
- Article
- Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila.PLoS genetics · 2021Article
- Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data.Molecular biology and evolution · 2020Article
- Co-opted transposons help perpetuate conserved higher-order chromosomal structures.Genome biology · 2020Article
- Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes.BMC evolutionary biology · 2019Article
- The Role of Chromatin Accessibility in cis-Regulatory Evolution.Genome biology and evolution · 2019Article
- Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- K-mer-Based Motif Analysis in Insect Species acrossComputational and mathematical methods in medicine · 2019Article
- Evidence for Stabilizing Selection Driving Mutational Turnover of Short Motifs in the Eukaryotic Complementary Sex Determiner (Csd) Protein.G3 (Bethesda, Md.) · 2018Article
- Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals.PLoS computational biology · 2018Article
85 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an evolutionary model to study binding-site turnover that uses multiple sequence alignments to assess the evolutionary constraint on individual binding sites, and to map gain and loss events along a phylogenetic tree. We apply this model to study the evolutionary dynamics of binding sites of the Drosophila melanogaster transcription factor Zeste, using genome-wide in vivo (ChIP-chip) binding data to identify functional Zeste binding sites, and the genome sequences of D. melanogaster, D. simulans, D. erecta, and D. yakuba to study their evolution. We estimate that more than 5% of functional Zeste binding sites in D. melanogaster were gained along the D. melanogaster lineage or lost along one of the other lineages. We find that Zeste-bound regions have a reduced rate of binding-site loss and an increased rate of binding-site gain relative to flanking sequences. Finally, we show that binding-site gains and losses are asymmetrically distributed with respect to D. melanogaster, consistent with lineage-specific acquisition and loss of Zeste-responsive regulatory elements.
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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.