000226079 001__ 226079
000226079 005__ 20181203024554.0
000226079 0247_ $$2doi$$a10.1038/nmeth.4143
000226079 022__ $$a1548-7105
000226079 02470 $$2ISI$$a000395661700032
000226079 037__ $$aARTICLE
000226079 245__ $$aSMiLE-seq identifies binding motifs of single and dimeric transcription factors
000226079 260__ $$bNature Publishing Group$$c2017$$aLondon
000226079 269__ $$a2017
000226079 300__ $$a12
000226079 336__ $$aJournal Articles
000226079 520__ $$aResolving 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.
000226079 700__ $$aIsakova, Alina
000226079 700__ $$0249526$$g183107$$aGroux, Romain
000226079 700__ $$aImbeault, Michael
000226079 700__ $$aRainer, Pernille
000226079 700__ $$aAlpern, Daniel
000226079 700__ $$aDainese, Riccardo
000226079 700__ $$0243605$$g176602$$aAmbrosini, Giovanna
000226079 700__ $$0240083$$g167919$$aTrono, Didier
000226079 700__ $$aBucher, Philipp$$g113607$$0244404
000226079 700__ $$aDeplancke, Bart
000226079 773__ $$j14$$tNature methods$$q316–322
000226079 909C0 $$xU11780$$0252244$$pGR-BUCHER
000226079 909C0 $$xU11172$$0252036$$pLVG
000226079 909CO $$pSV$$particle$$ooai:infoscience.tind.io:226079
000226079 917Z8 $$x169414
000226079 917Z8 $$x148230
000226079 937__ $$aEPFL-ARTICLE-226079
000226079 973__ $$rREVIEWED$$sPUBLISHED$$aEPFL
000226079 980__ $$aARTICLE