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Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches pp 13–31Cite as

The Application of Next Generation Sequencing Techniques to Plant Epigenomics

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Abstract

Epigenetic processes such as DNA methylation and the posttranslational modifications of histones play key roles in the regulation of plant development and in response and adaptation to the environment. The complexity of these processes means it is often beneficial to study epigenetic modifications and pathways in a systematic, genome-wide manner.

The first epigenomic investigations used microarrays to detect genomic regions enriched in chromatin immunoprecipitation or methylated DNA precipitation assays. More recently the epigenomics field has been revolutionized by the appearance of next generation sequencing (NGS) based methods, some of which were first applied to plants. These have improved sensitivity and vastly broadened the type of experiments that are feasible. As these methods are not restricted to the few model plants for which microarrays exist, they can be applied to study a wide variety of species.

This chapter will outline the use of, and experimental design for methods including whole-genome bisulfite sequencing, ChIP-sequencing, MNase-Seq and small RNA-sequencing. The downstream processing and analysis of data from epigenomics experiments is major component of all epigenomics investigations and some of the available approaches and tools available for these tasks will be discussed.

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Authors and Affiliations

  1. Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, Vienna, 1030, Austria

    Manu J. Dubin Ph.D.

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  1. Manu J. Dubin Ph.D.
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Correspondence to Manu J. Dubin Ph.D. .

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Editors and Affiliations

  1. Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy

    Gaurav Sablok

  2. Institute of Life Sciences, Nalco Square, Bhubaneswar, India

    Sunil Kumar

  3. Department of Forest Genetics, Forestry and Forest Products Research Institute (FFRI), Tsukuba, Ibaraki, Japan

    Saneyoshi Ueno

  4. Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan

    Jimmy Kuo

  5. Biodiversity and Molecular Ecology, Fondazione Edmund Mach, San Michele all'Adige, Italy

    Claudio Varotto

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Dubin, M.J. (2015). The Application of Next Generation Sequencing Techniques to Plant Epigenomics. In: Sablok, G., Kumar, S., Ueno, S., Kuo, J., Varotto, C. (eds) Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches. Springer, Cham. https://doi.org/10.1007/978-3-319-17157-9_2

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