Beyond motif recognition: Specificity of human transcription factors in yeast

Transcription factors (TFs) bind DNA through sequence-specific DNA-binding domains (DBDs), yet genome-wide analyses show that TFs occupy only a small fraction of their motif occurrences. This raises the question of how TFs distinguish specific targets from the many potential sites in the genome. To investigate determinants of binding specificity beyond the cognate motif and cofactor influences, we measured the binding of 60 human TFs across the budding yeast genome. Although human TFs robustly recognized their motifs, they displayed strong selectivity in site occupancy. Nucleosome abundance explained this selectivity only in part: among the 5-20% of motif sites that were bound, a substantial fraction remained nucleosome covered. Furthermore, TFs recognizing similar motif sequences independently localized to distinct subsets of sites within different promoters. Despite the absence of human-specific cofactors in yeast, both binding stability and genomic preferences depended on largely disordered non-DBD regions. These findings suggest intrinsically disordered regions (IDRs) may therefore direct genome binding TF target recognition across evolutionarily distant genomes.