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Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes

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Plant Synthetic Promoters

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1482))

Abstract

Bioinformatics tools can be employed to identify conserved cis-sequences in sets of coregulated plant genes because more and more gene expression and genomic sequence data become available. Knowledge on the specific cis-sequences, their enrichment and arrangement within promoters, facilitates the design of functional synthetic plant promoters that are responsive to specific stresses. The present chapter illustrates an example for the bioinformatic identification of conserved Arabidopsis thaliana cis-sequences enriched in drought stress-responsive genes. This workflow can be applied for the identification of cis-sequences in any sets of coregulated genes. The workflow includes detailed protocols to determine sets of coregulated genes, to extract the corresponding promoter sequences, and how to install and run a software package to identify overrepresented motifs. Further bioinformatic analyses that can be performed with the results are discussed.

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Acknowledgements

This work was supported by the Federal Ministry for Education and Research of Germany (BMBF) through grants 0315037B and 0315459A.

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Authors and Affiliations

  1. Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany

    Lorenz Bülow

  2. Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany

    Reinhard Hehl

Authors
  1. Lorenz Bülow
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  2. Reinhard Hehl
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Correspondence to Lorenz Bülow .

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Editors and Affiliations

  1. Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany

    Reinhard Hehl

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Bülow, L., Hehl, R. (2016). Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes. In: Hehl, R. (eds) Plant Synthetic Promoters. Methods in Molecular Biology, vol 1482. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6396-6_15

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  • DOI: https://doi.org/10.1007/978-1-4939-6396-6_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6394-2

  • Online ISBN: 978-1-4939-6396-6

  • eBook Packages: Springer Protocols

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