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 successfully drugged. 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 pockets where mutations have strong functional effects on binding, either within the binding interface or distant from it. Using TF-MAPS it should be possible to chart functional and allosteric maps for hundreds of human TFs and other DNA-binding proteins to understand DNA recognition and TF regulation, to mechanistically interpret clinical variants, and to guide the development of TF-modulating therapeutics.