Assessing Distribution and Variation of Genome-Wide DNA Methylation Using Short-Read Sequencing

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1610)

Abstract

DNA methylation is one of the most prominent epigenetic marks and is particularly complex in plant genomes. Whole-genome bisulfite sequencing (WGBS) using short reads has become the standard tool to study genome-wide patterns of DNA methylation. The goal of the present protocol is to enable readers to perform WGBS on both the wet lab and the computational side. We briefly outline important steps in bisulfite library preparation, then focus on the different aspects of DNA methylation analysis, from read mapping to identifying biologically relevant differential methylation between different samples.

Key words

DNA methylation Short-read sequencing Bisulfite Differential methylation Differentially methylated region 

Notes

Acknowledgments

This work was supported by the Max Planck Society.

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Computomics GmbHTübingenGermany
  2. 2.Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
  3. 3.Gregor Mendel InstituteAustrian Academy of Sciences, Vienna Biocenter (VBC)ViennaAustria

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