Advertisement

Whole-Genome Bisulfite Sequencing and Epigenetic Variation in Cereal Methylomes

  • Taiji KawakatsuEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2072)

Abstract

Whole-genome bisulfite sequencing (WGBS) is a technique used for the analysis of genome-wide DNA methylation patterns (DNA methylomes) at a single-base resolution. Here, I describe a simple DNA extraction method from rice endosperm and the universal protocol of WGBS, MethylC-sequencing library preparation. The use of benzyl chloride allows for the extraction of high-quality genomic DNA from starchy endosperm, while sodium bisulfite converts unmethylated cytosine to uracil, whereas methylated cytosine is unchanged. The bisulfite conversion of whole genome sequencing libraries before the final amplification step allows for the discrimination of methylated from unmethylated cytosines in a genome-wide manner.

Key words

DNA methylomes Rice Cereal Endosperm Whole-genome bisulfite sequencing MethylC-sequencing 

Notes

Acknowledgments

This work is supported by JSPS KAKENHI (17H05851 and 19H04873).

References

  1. 1.
    Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204–220CrossRefGoogle Scholar
  2. 2.
    Kawashima T, Berger F (2014) Epigenetic reprogramming in plant sexual reproduction. Nat Rev Genet 15:613–624CrossRefGoogle Scholar
  3. 3.
    Lister R, Ecker JR (2009) Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 19:959–966CrossRefGoogle Scholar
  4. 4.
    Lister R, O’Malley RC, Tonti-Filippini J et al (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536CrossRefGoogle Scholar
  5. 5.
    Urich MA, Nery JR, Lister R et al (2015) MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc 10:475–483CrossRefGoogle Scholar
  6. 6.
    Zemach A, Kim MY, Silva P et al (2010) Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A 107:18729–18734CrossRefGoogle Scholar
  7. 7.
    Lafon-Placette C, Hatorangan MR, Steige KA et al (2018) Paternally expressed imprinted genes associate with hybridization barriers in Capsella. Nat Plants 4:352–357CrossRefGoogle Scholar
  8. 8.
    Kinoshita T (2018) A parental tug-of-war. Nat Plants 4:329–330CrossRefGoogle Scholar
  9. 9.
    Zhu H, Qu F, Zhu LH (1993) Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride. Nucleic Acids Res 21:5279–5280CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Institute of Agrobiological Sciences, National Agriculture and Food Research OrganizationTsukubaJapan

Personalised recommendations