Methods such as ChIP–seq and CUT&RUN are used to identify transcription factor-binding sites in the genome, but do not inform on the biochemistry of transcription finding binding — and properties such as affinity and specificity are important for predicting the functional consequences of binding. Neikes et al. address this problem with binding affinities to native chromatin by sequencing (BANC-seq), a method that quantifies absolute binding affinity to chromatin in cellulo. A titration of exogenous Flag-tagged transcription factors was incubated with isolated nuclei and genome-wide binding was quantified using ChIP–seq or CUT&RUN. Epigenetic context has a strong effect on affinities, whereas motif sequence does not account for most variation, which suggests that these variants fine-tune affinity. Increasing transcription factor concentration broadens the affinity range within which a transcription factor can productively bind. Given the wealth of microscopy studies that show that the gene regulatory activity of transcription factors is related to biochemical properties such as binding affinity, high-throughput methods to quantify these properties are a crucial step towards a quantitative understanding of the gene regulatory networks of transcription factors and regulatory elements and how these underlie phenotypes.

ChIP–seq 和 CUT&RUN 等方法用于识别基因组中的转录因子结合位点，但不提供转录发现结合的生物化学信息——亲和力和特异性等特性对于预测结合的功能结果很重要。内克斯等人。通过测序 (BANC-seq) 通过对天然染色质的结合亲和力解决这个问题，这是一种量化纤维素中染色质的绝对结合亲和力的方法。外源性 Flag 标记转录因子的滴定与分离的细胞核一起孵育，并使用 ChIP–seq 或 CUT&RUN 量化全基因组结合。表观遗传背景对亲和力有很大影响，而基序序列并不能解释大多数变异，这表明这些变异微调了亲和力。增加转录因子浓度拓宽了转录因子可以有效结合的亲和力范围。鉴于大量显微镜研究表明转录因子的基因调控活性与结合亲和力等生化特性有关，因此量化这些特性的高通量方法是定量理解转录因子基因调控网络的关键一步和监管要素以及这些如何成为表型的基础。