ArticleNature biotechnology2015
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.
Article in Nature biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers.
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Who cites it
151 citing papers in PubMed, 285 citations in OpenAlex.
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- High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo.Research square · 2026Article
- Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells.G3 (Bethesda, Md.) · 2026Article
- From binding to networks: methods for identifying transcription factor targets in plant systems.Frontiers in plant science · 2026Review
- High-resolution binding data of TFIID and cofactors show promoter-specific differencesbioRxiv : the preprint server for biology · 2025Article
- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.Protein & cell · 2025Article
- Machine Learning-Driven Prediction of Spatiotemporal Dynamics of Active Nuclei DuringInternational journal of molecular sciences · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.Research square · 2025Article
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- ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network.Nature structural & molecular biology · 2025Article
- Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition.Nature structural & molecular biology · 2025Article
- DNA-Protein Binding is Dominated by Short Anchoring Elements.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genome-Wide Silencer Screening Reveals Key Silencer Modulating Reprogramming Efficiency in Mouse Induced Pluripotent Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II.Molecular systems biology · 2025Article
- Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model.Cell genomics · 2025Article
- Article
91 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins--human TBP and Drosophila NFkB, Twist and Max--shows that it outperforms existing ChIP protocols in resolution and specificity, pinpoints relevant binding sites within enhancers containing multiple binding motifs, and allows for the analysis of in vivo binding specificities. Notably, we show that Max frequently interacts with DNA sequences next to its motif, and that this binding pattern correlates with local DNA-sequence features such as DNA shape. ChIP-nexus will be broadly applicable to the study of in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms.
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