Project description:Sequence-specific DNA binding by transcription factors (TFs) is required for accurately regulating target gene expression. However, rules governing TF-DNA interactions remain elusive because current high-throughput approaches to map them fail to identify lower-affinity interactions. To address this gap, we have developed PADIT-seq, a novel technology to detect TF-DNA interactions across the entire spectrum of affinities. By profiling the binding preferences of Egr1 and Hoxd13 to all possible 10-mers, we found that nucleotides flanking high-affinity binding sites create additional, overlapping lower-affinity sites that together modulate TF genomic occupancy. The formation of these extended recognition sequences is enabled by an inherent property of TF binding sites to interweave together. Highlighting the importance of lower-affinity binding sites, we provide mechanistic insights into their role in fine-tuning gene regulation.
