Engineering intrinsically disordered regions for guiding genome navigation

Abstract

Intrinsically disordered regions (IDRs) navigate transcription factors (TFs) to their binding sites in genomes, raising the question of how IDR sequences can encode for specific genome recognition. To define the principles of IDR-directed binding, we designed de novo IDRs and tested their activity in directing selective binding across the budding yeast genome. Our de novo IDRs were designed by dispersing hydrophobic amino acids within hundreds of hydrophilic residues, as we found to be required in native TF-directing IDRs. Although showing no alignment-based similarity to native TFs, the de novo IDRs were active in directing genome binding toward a tunable range of targets, as revealed by systematically varying the hydrophobic spread or disorder scaffold. Overall, the 185 synthetic IDRs tested displayed a continuum of sequence-directed binding preferences across hundreds of promoters. Our results open new doors for understanding and engineering selective binding across genomes. © 2026 Elsevier Inc.