This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Method Article
SMiLE-seq: Selective Microfluidics-based Ligand Enrichment followed by sequencing
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
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.
Keywords
Microfluidics, Transcription Factor (TF), DNA binding motif, gene regulation, in vitro methods, high-throughput sequencing, semi-automated technology.
Figure 1
Figure 2
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 17 Jan, 2017
No community comments so far
Metrics
Comments: 0
HTML Views: ...
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)
Learn more about our company.
This is a preprint. It has not completed peer review.
Method Article
SMiLE-seq: Selective Microfluidics-based Ligand Enrichment followed by sequencing
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
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
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
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)