Journal
NATURE METHODS
Volume 14, Issue 3, Pages 316-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/NMETH.4143
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Funding
- Swiss National Science Foundation [31003A_162735, CRSII3_14768]
- SystemsX.ch Special Opportunity Project [2015/323]
- Swiss National Science Foundation (SNF) [31003A_162735] Funding Source: Swiss National Science Foundation (SNF)
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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 DNDNA-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.
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