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

DNA binding domains (DBDs) of transcription factors (TFs) bind
DNA sequence motifs that are highly abundant in genomes.
Within cells, TFs bind only a fraction of motif-containing sites,
following mechanisms encoded by DBDs or DBD-external
(nonDBD) sequences. Despite much interest, the relative roles
of DBDs and nonDBDs in distinguishing motif-containing sites
remains unknown. To examine that, we compared genome-
wide binding of 48 (~30%) budding yeast TFs with respective
DBD-only, DBD-lacking, and TF-truncation variants. With a few
exceptions, binding locations varied between DBDs and TFs, a
difference we map to the cumulative action of multiple
determinants distributed within mostly disordered nonDBD
regions. Contrasting the permissive promoter-selection of
DBD-only variants, nonDBDs restricted TF binding to promoters
of fuzzy nucleosome architecture, explaining a central
hallmark of budding yeast’s transcriptional network. We
conclude that DBDs and nonDBDs employ complementary DNA-
targeting strategies, which together define TF binding
specificity along genomes.