ArticleMolecular cell2024
Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1.
Article in Molecular cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- The Role of AP-1 in Cancer: Regulation, Tumor Microenvironment and Therapeutic Targeting.Biomolecules · 2026Review
- The CEBPB-AP-1 (JunB/Fos) Axis Drives Neuroinflammation and Microglial Dysfunction Via TNF Signaling in Ischemic Stroke.Inflammation · 2026Article
- Optimized optogenetic anti-CRISPR for endogenous gene regulation in Drosophila.Nucleic acids research · 2026Article
- TPCAV: Interpreting deep learning genomics models via concept attribution.bioRxiv : the preprint server for biology · 2026Article
- Epigenetic memory of colitis promotes tumour growth.Nature · 2026Article
- AP-1 promotes oncogenic transcription in lung cancer cells by bridging promoter-enhancer interactions.Cancer gene therapy · 2026Article
- Basis for lineage-determining pioneer factors targeting distinct repressed chromatin states.Science advances · 2026Article
- Mediator complex subunit MED23 dampens antiviral innate immunity by restricting RIG-I expression.PLoS biology · 2025Article
- Structural insights into the recognition of native nucleosomes by pioneer transcription factors.Current opinion in structural biology · 2025Review
- Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model.Cell genomics · 2025Article
- The RNA Revolution in the Central Molecular Biology Dogma Evolution.International journal of molecular sciences · 2024Review
- Exploring the reciprocity between pioneer factors and development.Development (Cambridge, England) · 2024Review
- Pioneer factors: nature or nurture?Critical reviews in biochemistry and molecular biologyReview
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8 authors.
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Abstract
Despite the unique ability of pioneer factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called chromatin immunoprecipitation with integrated synthetic oligonucleotides (ChIP-ISO) to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1, in human A549 cells. Combining ChIP-ISO with in vitro and neural network analyses, we find that (1) FOXA1 binding is strongly affected by co-binding transcription factors (TFs) AP-1 and CEBPB; (2) FOXA1 and AP-1 show binding cooperativity in vitro; (3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin; and (4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.
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