SMiLE-seq identifies binding motifs of single and dimeric transcription factors

Nat Methods. 2017 Mar;14(3):316-322. doi: 10.1038/nmeth.4143. Epub 2017 Jan 16.


Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq). SMiLE-seq is neither limited by DNA bait length nor biased toward strong affinity binders; it probes the DNA-binding properties of TFs over a wide affinity range in a fast and cost-effective fashion. We validated SMiLE-seq by analyzing 58 full-length human, mouse, and Drosophila TFs from distinct structural classes. All tested TFs yielded DNA-binding models with predictive power comparable to or greater than that of other in vitro assays. De novo motif discovery on all JUN-FOS heterodimers and several nuclear receptor-TF complexes provided novel insights into partner-specific heterodimer DNA-binding preferences. We also successfully analyzed the DNA-binding properties of uncharacterized human C2H2 zinc-finger proteins and validated several using ChIP-exo.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites / genetics
  • CYS2-HIS2 Zinc Fingers / physiology*
  • Computational Biology
  • DNA / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Drosophila / genetics
  • Gene Expression Regulation
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • JNK Mitogen-Activated Protein Kinases / genetics
  • JNK Mitogen-Activated Protein Kinases / metabolism*
  • Mice
  • Microfluidics / methods
  • Proto-Oncogene Proteins c-fos / genetics
  • Proto-Oncogene Proteins c-fos / metabolism*
  • Sequence Analysis, DNA / methods
  • Transcription Factors / metabolism*


  • DNA-Binding Proteins
  • Proto-Oncogene Proteins c-fos
  • Transcription Factors
  • DNA
  • JNK Mitogen-Activated Protein Kinases