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Plant Gene Regulatory Networks pp 239–269Cite as

Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development

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

Abstract

Key transcription factors (TFs) controlling the morphogenesis of flowers and leaves have been identified in the model plant Arabidopsis thaliana. Recent genome-wide approaches based on chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) enable systematic identification of genome-wide TF binding sites (TFBSs) of these regulators. Here, we describe a computational pipeline for analyzing ChIP-seq data to identify TFBSs and to characterize gene regulatory networks (GRNs) with applications to the regulatory studies of flower development. In particular, we provide step-by-step instructions on how to download, analyze, visualize, and integrate genome-wide data in order to construct GRNs for beginners of bioinformatics. The practical guide presented here is ready to apply to other similar ChIP-seq datasets to characterize GRNs of interest.

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Acknowledgments

K.K. wishes to thank the Alexander-von-Humboldt foundation and the BMBF for ongoing support.

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Authors and Affiliations

  1. Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 25, 14476, Potsdam, Germany

    Dijun Chen

  2. Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany

    Dijun Chen & Kerstin Kaufmann

Authors
  1. Dijun Chen
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  2. Kerstin Kaufmann
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Corresponding author

Correspondence to Dijun Chen .

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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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Chen, D., Kaufmann, K. (2017). Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development. 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_16

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  • DOI: https://doi.org/10.1007/978-1-4939-7125-1_16

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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

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