Neikes Hannah K, Kliza Katarzyna W, Gräwe Cathrin, Wester Roelof A, Jansen Pascal W T C, Lamers Lieke A, Baltissen Marijke P, van Heeringen Simon J, Logie Colin, Teichmann Sarah A, Lindeboom Rik G H, Vermeulen Michiel
Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands.
Nat Biotechnol. 2023 Dec;41(12):1801-1809. doi: 10.1038/s41587-023-01715-w. Epub 2023 Mar 27.
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.
全基因组范围内转录因子的结合受DNA序列和染色质特征调控。然而，目前尚无法量化染色质环境对转录因子结合亲和力的影响。在此，我们报告一种名为通过测序测定天然染色质结合亲和力（BANC-seq）的方法，以确定全基因组中转录因子与天然DNA的绝对表观结合亲和力。在BANC-seq中，将一系列浓度的标记转录因子添加到分离的细胞核中。然后对每个样本测量浓度依赖性结合，以量化全基因组范围内的表观结合亲和力。BANC-seq为转录因子生物学增加了一个定量维度，这使得能够基于转录因子浓度对基因组靶点进行分层，并预测非生理条件下（如疾病相关的（癌）基因过表达）的转录因子结合位点。值得注意的是，虽然转录因子的共有DNA结合基序对于建立高亲和力结合位点很重要，但在基因组中产生纳摩尔亲和力相互作用并不总是严格需要这些基序。
