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

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

Author information

1
Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
2
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
3
Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
4
Global Health Institute (GHI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

Abstract

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.

PMID:
28092692
DOI:
10.1038/nmeth.4143
[Indexed for MEDLINE]

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