Complementary strategies for directing in vivo transcription factor binding through DNA binding domains and intrinsically disordered regions

DNA binding domains (DBDs) of transcription factors (TFs) recognize DNA sequence motifs that are highly abundant in genomes. Within cells, TFs bind a subset of motif-containing sites as directed by either their DBDs or DBD-external (nonDBD) sequences. To define the relative roles of DBDs and nonDBDs in directing binding preferences, we compared the genome-wide binding of 48 (∼30%) budding yeast TFs with their DBD-only, nonDBD-truncated, and nonDBD-only mutants. With a few exceptions, binding locations differed between DBDs and TFs, resulting from the cumulative action of multiple determinants mapped mostly to disordered nonDBD regions. Furthermore, TFs’ preferences for promoters of the fuzzy nucleosome architecture were lost in DBD-only mutants, whose binding spread across promoters, implicating nonDBDs’ preferences in this hallmark of budding yeast regulatory design. We conclude that DBDs and nonDBDs employ complementary DNA-targeting strategies, whose balance defines TF binding specificity along genomes. [Display omitted] •Systematic truncations and genomic mapping define TF binding specificity determinants•Most TFs depend on many weak determinants distributed within long IDRs outside DBDs•TFs lacking DBDs often localize to specific genes, including the right targets•Disordered non-DBDs explain TF preference for binding promoters of fuzzy nucleosomes To define the molecular basis of transcription factor (TF) specificity, Kumar et al. dissected the binding determinants of 48 yeast TFs. Most TFs contained multiple weak specificity determinants distributed over long, intrinsically disordered regions outside their DNA binding domains (DBDs), which biased TF binding toward promoters with a distinct nucleosome architecture.