ArticleScience (New York, N.Y.)2010
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.
Article in Science (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 468 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.
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
468 citing papers in PubMed, 1 synthesis or guideline pooled it, 733 citations in OpenAlex.
- ChIP-Hub provides an integrative platform for exploring plant regulome.Nature communications · 2022Pooled it
- Alignment-free integration of single-nucleus ATAC-seq across species with sPYce.Nature ecology & evolution · 2026Article
- IL-6-induced C/EBPα drives follicular regulatory T cell differentiation to regulate humoral immunity in mice.Nature communications · 2026Article
- Gene regulatory networks: from correlative models to causal explanations.Nature reviews. Genetics · 2026Review
- Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes.bioRxiv : the preprint server for biology · 2026Article
- Exonic enhancers are a widespread class of dual-function regulatory elements.Nature communications · 2026Article
- The molecular evolution of vertebrate organs.Nature ecology & evolution · 2026Review
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- Evolutionary Transitions in Social Behavior are Associated With Convergent and Partially Reversible Expansions of Transcription Factor Binding Sites.Genome biology and evolution · 2026Article
- Decoding thebioRxiv : the preprint server for biology · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Romantic love as regulatory co-option of maternal-bonding circuitry: a testable genetic account.Frontiers in behavioral neuroscience · 2026Article
- Article
- Deciphering the cucumber ATG6 and its promoter to enhance abiotic stress tolerance and drive stress-responsive transgene expression in plants.Transgenic research · 2025Article
- OptimDase: An Algorithm for Predicting DNA Binding Sites with Combined Feature Encoding.Interdisciplinary sciences, computational life sciences · 2025Article
- Motif-based models accurately predict cell type-specific distal regulatory elements.Nature communications · 2025Article
- "Frustratingly easy" domain adaptation for cross-species transcription factor binding prediction.bioRxiv : the preprint server for biology · 2025Article
- Recruitment, rewiring and deep conservation in flowering plant gene regulation.Nature plants · 2025Article
- Functional dissection of noncoding variants associated with rheumatoid arthritis.Annals of the rheumatic diseases · 2025Article
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
408 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
Abstract
Transcription factors (TFs) direct gene expression by binding to DNA regulatory regions. To explore the evolution of gene regulation, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine experimentally the genome-wide occupancy of two TFs, CCAAT/enhancer-binding protein alpha and hepatocyte nuclear factor 4 alpha, in the livers of five vertebrates. Although each TF displays highly conserved DNA binding preferences, most binding is species-specific, and aligned binding events present in all five species are rare. Regions near genes with expression levels that are dependent on a TF are often bound by the TF in multiple species yet show no enhanced DNA sequence constraint. Binding divergence between species can be largely explained by sequence changes to the bound motifs. Among the binding events lost in one lineage, only half are recovered by another binding event within 10 kilobases. Our results reveal large interspecies differences in transcriptional regulation and provide insight into regulatory evolution.
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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.