Hannah Neikes
Hannah Neikes

New method to profile transcription factor binding affinities across the genome

Hannah Neikes, Rik Lindeboom, Michiel Vermeulen and their colleagues have developed a new method called BANC-seq (Binding Affinities to Native Chromatin by sequencing) that allows them to measure the binding affinities of transcription factors (TFs) to DNA sequences in the genome. TF binding is crucial for regulating gene expression and cell fate, and dysregulation of TF-mediated gene expression is often associated with diseases like cancer. Existing sequencing-based methods can profile TF binding specificity and the epigenetic landscape, but they don't provide information about the absolute binding affinities. BANC-seq overcomes this limitation by quantifying TF binding affinities to native, chromatinized DNA. BANC-seq offers valuable insights into TF biology, enabling better understanding of pathological conditions and potential stratification of TF binding sites. The findings were published in Nature Biotechnology.

Binding affinities

In recent years, various sequencing-based methods have been developed to profile the epigenetic landscape and transcription factor binding specificity across the genome. However, to biochemically understand transcription factor binding, the binding affinity – i.e. the TF concentration required for specific binding – of a transcription factor for DNA sequences in the genome must also be considered. However, no existing technology is capable of quantifying absolute transcription factor binding affinities to native, chromatinized DNA. Therefore, Radboud researchers Hannah Neikes, Rik Lindeboom, Michiel Vermeulen and their colleagues developed a method to determine Binding Affinities to Native Chromatin by sequencing or BANC-seq.


In BANC-seq, a concentration range of a tagged transcription factor is added to isolated nucleic from mammalian cells. Concentration dependent binding for each titration point is then measured to quantify binding affinities across the genome. BANC-seq revealed that, by and large, accessible chromatin is a pre-requisite for high and low affinity transcription factor binding to occur in a specific epigenetic state. Furthermore, changes in chromatin context during cellular differentiation result in cell type-specific transcription factor binding affinities. Interestingly however, chromatin context is interpreted differently by the pioneering transcription factor FOXA1 compared to YY1, SP1 or MYC. Notably, whereas consensus DNA binding motifs for TFs are important to establish high-affinity binding sites in the genome, these motifs are not always strictly required to generate nanomolar affinity interactions in the genome.  

In summary, BANC-seq adds a much needed quantitative dimension to transcription factor biology and enables stratification of transcription factor binding sites in pathological conditions, such as over-expression of oncogenes in cancer.