ArticleNature structural & molecular biology2025
DNA bendability regulates transcription factor binding to nucleosomes.
Article in Nature structural & molecular biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes.bioRxiv : the preprint server for biology · 2026Article
- DNA Mechanical Strain Steers Transcription Factor Recognition.Research square · 2026Article
- Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion.bioRxiv : the preprint server for biology · 2026Article
- PIONEARing how DNA sequence composition tunes TF-nucleosome interactions.Nature reviews. Molecular cell biology · 2026Article
- Basis for lineage-determining pioneer factors targeting distinct repressed chromatin states.Science advances · 2026Article
- Uncovering the Mechanistic Landscape of Regulatory DNA with Deep Learning.bioRxiv : the preprint server for biology · 2025Article
- Structural insights into the recognition of native nucleosomes by pioneer transcription factors.Current opinion in structural biology · 2025Review
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Abstract
Cell fates are controlled by 'pioneers', sequence-specific transcription factors (TFs) that bind recognition motifs on nucleosomes ('pioneer binding'). Pioneers occupy a minority of their recognition sequences in the genome, suggesting that the sequence context regulates their binding. Here we developed PIONEAR-seq, a high-throughput biochemical assay to characterize pioneer binding. We used PIONEAR-seq to assay 11 human TFs for binding to nucleosomes based on Widom 601 versus genomic sequences. We found that pioneer binding, while mediated primarily by the recognition motifs of TFs, is regulated by the broader nucleosome sequence context. Certain TFs, found to be dyad or periodic binders on nucleosomes assembled on synthetic sequences, exhibited end binding to nucleosomes based on genomic sequences. We propose a model where the local bendability of the DNA sequence in nucleosomes is involved in positioning pioneer binding, and thus represents another cis-regulatory layer in eukaryotic genomes.
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