De Novo Identification and Biophysical Characterization of Transcription Factor Binding Sites with Microfluidic Affinity Analysis

Gene expression is regulated in part by protein transcription factors (TFs) that bind target regulatory DNA sequences. Predicting DNA binding sites and affinities from transcription factor sequence or structure is difficult; therefore, experimental data are required to link TFs to target sequences. We present a microfluidics-based approach for de novo discovery and quantitative biophysical characterization of DNA target sequences. We validated our technique by measuring sequence preferences for 28 S. cerevisiae TFs with a variety of DNA binding domains, including several that have proven difficult to study via other techniques. For each TF, we measured relative binding affinities to oligonucleotides covering all possible 8-bp DNA sequences to create a comprehensive map of sequence preferences; for 4 TFs, we also determined absolute affinities. We anticipate that these data and future use of this technique will provide information essential for understanding TF specificity, improving identification of regulatory sites, and reconstructing regulatory interactions.