ArticleNature biotechnology2023
Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 26 citations in OpenAlex.
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- Age-independent and targetable transcription factor networks regulating CD8Cell reports · 2026Article
- Mechanisms and therapeutic prospects of DNA methylation-mucosal innate immunity crosstalk in inflammatory bowel disease.Frontiers in immunology · 2026Review
- Precise modulation of BRG1 levels reveals features of mSWI/SNF dosage sensitivity.Nature genetics · 2025Article
- Transcriptional regulation as a dose-dependent process: insights from transcription factor tuning.Open biology · 2025Review
- An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin.bioRxiv : the preprint server for biology · 2025Article
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- Rethinking chromatin accessibility: from compaction to dynamic interactions.Current opinion in genetics & development · 2025Review
- Quantifying genome-wide transcription factor binding affinities for chromatin using BANC-seq.Nature protocols · 2024Article
- Context transcription factors establish cooperative environments and mediate enhancer communication.Nature genetics · 2024Article
- Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1.Molecular cell · 2024Article
- Pioneer factors - key regulators of chromatin and gene expression.Nature reviews. Genetics · 2023Article
- Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1.bioRxiv : the preprint server for biology · 2023Article
- Gene regulatory network inference in the era of single-cell multi-omics.Nature reviews. Genetics · 2023Review
- Determining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy.Journal of proteome research · 2023Article
- A variegated model of transcription factor function in the immune system.Trends in immunology · 2023Review
- Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0.Scientific reports · 2023Article
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Authors and funding
12 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factor binding across the genome is regulated by DNA sequence and chromatin features. However, it is not yet possible to quantify the impact of chromatin context on transcription factor binding affinities. Here, we report a method called binding affinities to native chromatin by sequencing (BANC-seq) to determine absolute apparent binding affinities of transcription factors to native DNA across the genome. In BANC-seq, a concentration range of a tagged transcription factor is added to isolated nuclei. Concentration-dependent binding is then measured per sample to quantify apparent binding affinities across the genome. BANC-seq adds a quantitative dimension to transcription factor biology, which enables stratification of genomic targets based on transcription factor concentration and prediction of transcription factor binding sites under non-physiological conditions, such as disease-associated overexpression of (onco)genes. Notably, whereas consensus DNA binding motifs for transcription factors are important to establish high-affinity binding sites, these motifs are not always strictly required to generate nanomolar-affinity interactions in the genome.
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