GSE193553
BANCseq for determination of genome-wide apparent transcription factor binding affinities [CUT&Run]
In vivo transcription factor binding is regulated by DNA sequence and chromatin features. However, the impact of chromatin context on genome-wide transcription factor binding affinities have not yet been characterized. Here we report the establishment of a quantitative protein-DNA binding assay to determine genome-wide binding affinities to native chromatinized DNA. We use this method to quantify apparent genome-wide binding affinities of both pioneering and non-pioneering transcription factors to uncover the regulatory role of chromatin on transcription factor binding. This revealed that DNA accessibility is the main determinant of transcription factor binding, which restricts nanomolar binding of non-pioneering factors to promoters. DNA binding motifs only appear to be important for very high-affinity binding, but are not essential for nanomolar binding. We uncover numerous biological processes enriched at specific binding affinities, suggesting they are regulated at defined transcription factor concentrations. Importantly, our method adds a new quantitative layer of transcription factor biology, enabling stratification of genomic targets based on transcription factor expression and prediction of transcription factor binding sites under non-physiological conditions, such as disease associated elevated expression of (onco)genes. Overall design: Quantification of genome wide apparent transcription factor Binding Affinities in Native Chromatin by BANC-seq was performed in human cell line MCF-7, R1 mouse embryonic stem cells (mESC), R1 neural progenitor cells (NPC), and mESC hybrid (F121, Castaneus and 129/Sv) for transcription factors YY1, FOXA1, SP1 and cMYC-MAX complex.