Abstract
We present a method through which one may monitor the relative binding affinity of a given protein to DNA motifs on the scale of a whole genome. Briefly, the protein of interest is incubated with fragmented genomic DNA and then affixed to a column. Washes with buffers containing low salt concentrations will remove nonbound DNA fragments, while stepwise washes with increasing salt concentrations will elute more specifically bound fragments. Massive sequencing is used to identify eluted DNA fragments and map them on the genome, which permits us to classify the different binding sites according to their affinity and determine corresponding consensus motifs (if any).
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Acknowledgments
This work was supported by the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013 grant agreement no. 281590) to F.-X.B.
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Poidevin, M., Galli, E., Yamaichi, Y., Barre, FX. (2017). WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites. In: Espéli, O. (eds) The Bacterial Nucleoid. Methods in Molecular Biology, vol 1624. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7098-8_5
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DOI: https://doi.org/10.1007/978-1-4939-7098-8_5
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Publisher Name: Humana Press, New York, NY
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Online ISBN: 978-1-4939-7098-8
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