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Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information

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Plant Gene Regulatory Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2698))

Abstract

Gene regulatory networks (GRNs) represent the regulatory links between transcription factors (TF) and their target genes. In plants, they are essential to understand transcriptional programs that control important agricultural traits such as yield or (a)biotic stress response. Although several high- and low-throughput experimental methods have been developed to map GRNs in plants, these are sometimes expensive, come with laborious protocols, and are not always optimized for tomato, one of the most important horticultural crops worldwide. In this chapter, we present a computational method that covers two protocols: one protocol to map gene identifiers between two different tomato genome assemblies, and another protocol to predict putative regulators and delineate GRNs given a set of functionally related or coregulated genes by exploiting publicly available TF-binding information. As an example, we applied the motif enrichment protocol on tomato using upregulated genes in response to jasmonate, as well as upregulated and downregulated genes in plants with genotypes OENAM1 and nam1, respectively. We found that our protocol accurately infers the expected TFs as top enriched regulators and identifies GRNs functionally enriched in biological processes related with the experimental context under study.

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Acknowledgments

This work was supported by a Bijzonder Onderzoeksfonds grant from Ghent University [BOF24Y2019001901] to NMP.

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Authors and Affiliations

  1. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

    Nicolás Manosalva Pérez & Klaas Vandepoele

  2. Center for Plant Systems Biology, VIB, Ghent, Belgium

    Nicolás Manosalva Pérez & Klaas Vandepoele

  3. Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium

    Klaas Vandepoele

Authors
  1. Nicolás Manosalva Pérez
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  2. Klaas Vandepoele
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Correspondence to Klaas Vandepoele .

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Editors and Affiliations

  1. Berlin, Germany

    Kerstin Kaufmann

  2. Ghent, Belgium

    Klaas Vandepoele

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Manosalva Pérez, N., Vandepoele, K. (2023). Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information. In: Kaufmann, K., Vandepoele, K. (eds) Plant Gene Regulatory Networks. Methods in Molecular Biology, vol 2698. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3354-0_19

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  • DOI: https://doi.org/10.1007/978-1-0716-3354-0_19

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3353-3

  • Online ISBN: 978-1-0716-3354-0

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