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Plant Epigenetics and Epigenomics pp 15–31Cite as

Approaches to Whole-Genome Methylome Analysis in Plants

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2093))

Abstract

Cytosine methylation as a reversible chromatin mark has been investigated extensively for its influence on gene silencing and the regulation of its dynamic association–disassociation at specific sites within a eukaryotic genome. With the remarkable reductions in cost and time associated with whole-genome DNA sequence analysis, coupled with the high fidelity of bisulfite-treated DNA sequencing, single nucleotide resolution of cytosine methylation repatterning within even very large genomes is increasingly achievable. What remains a challenge is the analysis of genome-wide methylome datasets and, consequently, a clear understanding of the overall influence of methylation repatterning on gene expression or vice versa. Reported data have sometimes been subject to stringent data filtering methods that can serve to skew downstream biological interpretation. These complications derive from methylome analysis procedures that vary widely in method and parameter setting. DNA methylation as a chromatin feature that influences DNA stability can be dynamic and rapidly responsive to environmental change. Consequently, methods to discriminate background “noise” of the system from biological signal in response to specific perturbation is essential in some types of experiments. We describe numerous aspects of whole-genome bisulfite sequence data that must be contemplated as well as the various steps of methylome data analysis which impact the biological interpretation of the final output.

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  1. Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA, USA

    Xiaodong Yang & Sally A. Mackenzie

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  1. Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland

    Charles Spillane

  2. Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland Galway (NUI Galway), Galway, Ireland

    Peter McKeown

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Yang, X., Mackenzie, S.A. (2020). Approaches to Whole-Genome Methylome Analysis in Plants. In: Spillane, C., McKeown, P. (eds) Plant Epigenetics and Epigenomics . Methods in Molecular Biology, vol 2093. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0179-2_2

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  • DOI: https://doi.org/10.1007/978-1-0716-0179-2_2

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0178-5

  • Online ISBN: 978-1-0716-0179-2

  • eBook Packages: Springer Protocols

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