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Selecting Hypomethylated Genomic Regions Using MRE-Seq

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Plant Synthetic Promoters

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

Abstract

Here, we describe a method capable of filtering the hypomethylated part of plant genomes, the so-called hypomethylome. The principle of the method is based on the filtration and sequence analysis of small DNA fragments generated by methylation-sensitive four-cutter restriction endonucleases, possessing (5me)CpG motifs in their recognition sites. The majority of these fragments represent genes and their flanking regions containing also regulatory elements—the gene space of the genome. Besides the enrichment of the gene space, another advantage of the method is the simultaneous depletion of repetitive elements due to their methylated nature and its easy application on complex and large plant genomes. Additionally to the wet lab procedure, we describe how to analyze the data using bioinformatics methods and how to apply the method to comparative studies.

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Acknowledgements

This work was supported by the AIT Austrian Institute of Technology GmbH.

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Authors and Affiliations

  1. AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Street 24, 3430, Tulln, Austria

    Elisabeth Wischnitzki, Kornel Burg, Maria Berenyi & Eva Maria Sehr

Authors
  1. Elisabeth Wischnitzki
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  2. Kornel Burg
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  3. Maria Berenyi
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  4. Eva Maria Sehr
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Corresponding author

Correspondence to Elisabeth Wischnitzki .

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Editors and Affiliations

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

    Reinhard Hehl

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Wischnitzki, E., Burg, K., Berenyi, M., Sehr, E.M. (2016). Selecting Hypomethylated Genomic Regions Using MRE-Seq. 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_6

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  • DOI: https://doi.org/10.1007/978-1-4939-6396-6_6

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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

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