fast high-resolution functional and allosteric mapping of DNA-binding proteins

Transcription factors (TFs) bind specific DNA sequences to control gene expression. Inhibiting or modulating TF activity is of considerable therapeutic interest but very challenging because direct inhibition of DNA-binding interfaces with small molecules is rarely feasible, necessitating the development of allosteric modulators. The vast majority of TFs, however, have no known allosteric ligands or allosteric sites. Here, we introduce TF-MAPs, a scalable experimental platform that generates comprehensive functional and allosteric maps of DNA-binding proteins and we present the first three allosteric maps of human TFs. We first apply TF-MAPs to HNF1A to understand DNA recognition, allostery, and diabetes-causing mutations. We then use TF-MAPs to produce comparative maps for two forkhead TFs, FOXG1 and FOXP1. Allostery in all three proteins shows distance-dependent decay and anisotropy. The maps also identify allosteric surface sites and prioritise potentially druggable allosteric surface pockets. Using this approach it should be possible to chart functional and allosteric maps for hundreds of human TFs and other DNA-binding proteins to guide the interpretation of clinical variants and the development of therapeutics.