title: SMiLE-seq identifies binding motifs of single and dimeric transcription factors.
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.
authors.affiliation: Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Alina
authors.initials: A
authors.lastname: Isakova
authors.affiliation: Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.|Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Romain
authors.initials: R
authors.lastname: Groux
authors.affiliation: Global Health Institute (GHI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Michael
authors.initials: M
authors.lastname: Imbeault
authors.affiliation: Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Pernille
authors.initials: P
authors.lastname: Rainer
authors.affiliation: Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Daniel
authors.identifier: 0000-0002-4023-9652
authors.initials: D
authors.lastname: Alpern
authors.affiliation: Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Dainese
authors.affiliation: Swiss Institute of Bioinformatics, Lausanne, Switzerland.|Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Giovanna
authors.initials: G
authors.lastname: Ambrosini
authors.affiliation: Global Health Institute (GHI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Didier
authors.initials: D
authors.lastname: Trono
authors.affiliation: Swiss Institute of Bioinformatics, Lausanne, Switzerland.|Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
authors.affiliation: Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Bart
authors.initials: B
authors.lastname: Deplancke
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D000070580:CYS2-HIS2 Zinc Fingers / Q000502:physiology*; D019295:Computational Biology; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004330:Drosophila / Q000235:genetics; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D048031:JNK Mitogen-Activated Protein Kinases / Q000235:genetics / Q000378:metabolism*; D051379:Mice; D044085:Microfluidics / Q000379:methods; D016760:Proto-Oncogene Proteins c-fos / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D016760:Proto-Oncogene Proteins c-fos; D014157:Transcription Factors; D004247:DNA; D048031:JNK Mitogen-Activated Protein Kinases