ArticleTrends in genetics : TIG2009
Different gene regulation strategies revealed by analysis of binding motifs.
Article in Trends in genetics : TIG, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 164 papers.
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Who cites it
164 citing papers in PubMed, 303 citations in OpenAlex.
- GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors.Nature methods · 2026Article
- Nucleosomes and IDRs suppress promiscuous GCN4 binding on minichromosomes.Nature structural & molecular biology · 2026Article
- Evolutionary Simulations Reveal Role for Genomic Recombination in the Evolution of Gene Regulatory Network Complexity and Robustness.Genome biology and evolution · 2026Article
- Emergence Biases in Molecular Evolution.Genome biology and evolution · 2026Review
- NovelbioRxiv : the preprint server for biology · 2026Article
- Elevated MyoD1 levels expand genome-wide binding and the repertoire of regulated genes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Unstructured transcription factor interactions enable emergent specificity.Science (New York, N.Y.) · 2026Article
- Article
- EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.Briefings in bioinformatics · 2026Article
- Conservation of cis-regulatory codes over half a billion years of evolution.Science advances · 2025Article
- The transcriptomics of phenotypic nonspecificity in Drosophila melanogaster.G3 (Bethesda, Md.) · 2025Article
- Chromatin-dependent motif syntax defines differentiation trajectories.Molecular cell · 2025Article
- Article
- Intrinsically disordered regions as facilitators of the transcription factor target search.Nature reviews. Genetics · 2025Review
- DNA-Protein Binding is Dominated by Short Anchoring Elements.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- Article
- Chromatin enables precise and scalable gene regulation with factors of limited specificity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
104 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Coordinated regulation of gene expression relies on transcription factors (TFs) binding to specific DNA sites. Our large-scale information-theoretical analysis of > 950 TF-binding motifs demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations. Although bacterial TFs can recognize a specific DNA site in the genomic background, eukaryotic TFs exhibit widespread, nonfunctional binding and require clustering of sites to achieve specificity. We find support for this mechanism in a range of experimental studies and in our evolutionary analysis of DNA-binding domains. Our systematic characterization of binding motifs provides a quantitative assessment of the differences in transcription regulation in prokaryotes and eukaryotes.
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Registered trials
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