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Plant Epigenetics pp 445–462Cite as

Epigenetic Characterization of Satellite DNA in Sugar Beet (Beta vulgaris)

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Part of the book series: RNA Technologies ((RNATECHN))

Abstract

Satellite DNA is a major and abundant component of plant genomes and comprises important genomic regions such as heterochromatic knobs and centromeric chromatin. However, technical barriers of assembling first- and second-generation sequencing data hampered the complete arrangement of satellite DNAs in current plant genome sequences. Consequently, heterochromatic and centromeric regions possessing satellite DNA lack detailed characterization and assignment, which limits knowledge about their epigenetic status. We applied methods to overcome these limitations and to gain insight into the epigenetic modifications of satellite DNA-rich heterochromatic and centromeric regions of the sugar beet (Beta vulgaris) genome. Sugar beet is an important crop of temperate climate zones, which provides nearly 30% of the world’s annual sugar needs. Due to the 11% of the genome consisting of satellite DNAs, sugar beet is a suitable research object for comparative investigation and epigenetic characterization of this repeat class. We analyzed the epigenetic modifications of satellite DNA by using bisulfite sequencing, chromatin immunoprecipitation followed by sequencing (ChiP-Seq) using antibodies against histone CenH3 and dimethylated H3K9me2, and small RNA-seq data. Immunostaining of methylated cytosines and histone modifications combined with fluorescent in situ hybridization (FISH) coupled with super-resolution fluorescence microscopy complemented the epigenetic analysis. As a result, we uncovered individual epigenetic characteristics of plant satellite DNAs at high resolution and hypothesized a model for satellite DNA-directed heterochromatization.

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Acknowledgments

This work was supported by the BMBF grant “AnnoBeet: Annotation des Genoms der Zuckerrübe unter Berücksichtigung von Genfunktionen und struktureller Variabilität für Nutzung von Genomdaten in der Pflanzenbiotechnologie.”, FKZ-0315962-C to Thomas Schmidt.

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  1. Department of Biology, Technische Universität Dresden, 01062, Dresden, Germany

    Falk Zakrzewski & Thomas Schmidt

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  1. Falk Zakrzewski
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  2. Thomas Schmidt
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Correspondence to Thomas Schmidt .

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  1. Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany

    Nikolaus Rajewsky

  2. Nanobiomedical Center, Adam Mickiewicz University, Poznań, Poland

    Stefan Jurga

  3. Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

    Jan Barciszewski

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Zakrzewski, F., Schmidt, T. (2017). Epigenetic Characterization of Satellite DNA in Sugar Beet (Beta vulgaris). In: Rajewsky, N., Jurga, S., Barciszewski, J. (eds) Plant Epigenetics. RNA Technologies. Springer, Cham. https://doi.org/10.1007/978-3-319-55520-1_22

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