HT-SELEX data for: GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity of human transcription factors

A long-standing challenge in human regulatory genomics is that transcription factor (TF) DNA binding motifs are short and degenerate, while the genome is large. Motif scans therefore produce many false-positive binding site predictions. Using cyclic in vitro selections with fragmented, naked, and unmodified genomic DNA – a method we term GHT-SELEX (Genomic HT-SELEX) - we find that many human TFs possess much higher sequence specificity than current motif models imply. Instead, genomic binding profiles from GHT-SELEX are often surprisingly similar to those obtained in vivo (i.e. ChIP-seq peaks). The augmented specificity can be accounted for by at least three different factors: derivation and use of the motifs, multiple local matches in the motif scans, and alternative engagement of multiple DNA-binding domains within the same protein. In particular, long C2H2 zinc finger proteins often utilize modular DNA recognition, engaging different subsets of their DNA binding domain (DBD) arrays to recognize multiple types of distinct target sites, often evolving via internal duplication and divergence of one or more DBDs. Thus, contrary to conventional wisdom, TFs often possess sufficient intrinsic specificity to independently delineate cellular targets.