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Method Article
Bart Deplancke
Deplancke Lab, EPFL. Laboratory of System Biology and Genetics, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
Corresponding Author
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This work is licensed under a CC BY-NC 3.0 License. Read Full License
Selective Microfluidics-based Ligand Enrichment followed by sequencing (SMiLE-seq) is a rapid, semi-automated method aimed at resolving the DNA binding specificities of full-length transcription factors (TFs). The core of SMiLE-seq is a cross talk-devoid microfluidic platform that performs selection of DNA that is specifically bound to TFs from a pool of randomized DNA. Coupled to high-throughput sequencing, this platform allows the characterization of TF DNA binding preferences at an unprecedented resolution in just a single day. Unlike other, already established in vitro technologies that also aim to determine TF binding specificities, SMiLE-seq operates at micro scale and requires minute amounts of biological material. Moreover, it produces specificity models that characterize even low-affinity and transient molecular interactions and that have equal to superior predictive power than previously reported motifs. Finally, SMiLE-seq enables motif detection for monomers, homodimers, as well as heterodimers. SMiLE-seq should therefore prove highly valuable in deriving unbiased quantitative specificity models for single and dimeric, full-length TFs.
Keywords
Microfluidics, Transcription Factor (TF), DNA binding motif, gene regulation, in vitro methods, high-throughput sequencing, semi-automated technology.
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The authors declare no competing financial interests.
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Associated Publications
SMiLE-seq identifies binding motifs of single and dimeric transcription factors
by Alina Isakova, Romain Groux, Michael Imbeault, +7
Nature Methods (17 January, 2017)
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Bart Deplancke
Deplancke Lab, EPFL. Laboratory of System Biology and Genetics, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 17 Jan, 2017
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
Selective Microfluidics-based Ligand Enrichment followed by sequencing (SMiLE-seq) is a rapid, semi-automated method aimed at resolving the DNA binding specificities of full-length transcription factors (TFs). The core of SMiLE-seq is a cross talk-devoid microfluidic platform that performs selection of DNA that is specifically bound to TFs from a pool of randomized DNA. Coupled to high-throughput sequencing, this platform allows the characterization of TF DNA binding preferences at an unprecedented resolution in just a single day. Unlike other, already established in vitro technologies that also aim to determine TF binding specificities, SMiLE-seq operates at micro scale and requires minute amounts of biological material. Moreover, it produces specificity models that characterize even low-affinity and transient molecular interactions and that have equal to superior predictive power than previously reported motifs. Finally, SMiLE-seq enables motif detection for monomers, homodimers, as well as heterodimers. SMiLE-seq should therefore prove highly valuable in deriving unbiased quantitative specificity models for single and dimeric, full-length TFs.
Figure 1
Figure 2
The authors declare no competing financial interests.
Loading...
Associated Publications
SMiLE-seq identifies binding motifs of single and dimeric transcription factors
by Alina Isakova, Romain Groux, Michael Imbeault, +7
Nature Methods (17 January, 2017)