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

Abstract Transcription factors (TFs) bind specific DNA sequences to control gene expression. Modulating TF activity is of considerable therapeutic interest but very few TFs have been drugged successfully. TF DNA-binding interfaces are large and most TFs have no known allosteric ligands or allosteric sites. Here we introduce TF-MAPs, a scalable and general platform to chart complete functional maps of sequence-specific DNA-binding proteins. We apply TF-MAPS to three human disease TFs: HNF1A, FOXG1 and FOXP1. Allostery in all three proteins is distance-dependent, anisotropic and couples the DNA-binding interface to the protein surface. The allosteric surfaces of FOXG1 and FOXP1 are quite diverged, revealing a potential for protein-specific regulation in protein families. All three TFs have potentially druggable small pockets where mutations affect DNA binding, either within the binding interface or distant from it. Application of TF-MAPS will potentially lead to charting functional and allosteric maps for hundreds of human TFs and other DNA-binding proteins to understand DNA recognition and TF regulation, to interpret clinical variants mechanistically and to guide the development of TF-modulating therapeutics.