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SELEX-Seq: A Method to Determine DNA Binding Specificities of Plant Transcription Factors

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Plant Gene Regulatory Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1629))

Abstract

Systematic evolution of ligands by exponential enrichment (SELEX) is a method that allows isolating specific nucleotide sequences that interact with a DNA binding protein of choice. By using a transcription factor (TF) and a randomized pool of double-stranded DNA, this technique can be used to characterize TF DNA binding specificities and affinities. The method is based on protein-DNA complex immunoprecipitation with protein-specific antibodies and subsequent DNA selection and amplification. Application of massively parallel sequencing (-seq) at each cycle of SELEX allows determining the relative affinities to any DNA sequence for any transcription factor or TF complex. The resulting TF DNA binding motifs can be used to predict potential DNA binding sites in genomes and thereby direct target genes of TFs.

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Acknowledgments

We would like to thank Arttu Jolma and Jussi Taipale for providing barcoded ssDNA libraries and sharing details on the dsDNA library preparation and amplification. This work was supported by an NWO-VIDI grant to KK.

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Authors and Affiliations

  1. Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands

    Cezary Smaczniak & Gerco C. Angenent

  2. Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Berlin, Germany

    Cezary Smaczniak & Kerstin Kaufmann

  3. Bioscience, Wageningen Plant Research, Wageningen, The Netherlands

    Gerco C. Angenent

Authors
  1. Cezary Smaczniak
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  2. Gerco C. Angenent
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  3. Kerstin Kaufmann
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Corresponding author

Correspondence to Kerstin Kaufmann .

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Editors and Affiliations

  1. Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany

    Kerstin Kaufmann

  2. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Bernd Mueller-Roeber

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Smaczniak, C., Angenent, G.C., Kaufmann, K. (2017). SELEX-Seq: A Method to Determine DNA Binding Specificities of Plant Transcription Factors. In: Kaufmann, K., Mueller-Roeber, B. (eds) Plant Gene Regulatory Networks. Methods in Molecular Biology, vol 1629. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7125-1_6

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  • DOI: https://doi.org/10.1007/978-1-4939-7125-1_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7124-4

  • Online ISBN: 978-1-4939-7125-1

  • eBook Packages: Springer Protocols

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