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Methods Mol Biol. 2017;1610:61-72. doi: 10.1007/978-1-4939-7003-2_5.

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

Author information

1
Computomics GmbH, Christophstr. 32, 72072, Tübingen, Germany.
2
Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany. claude.becker@gmi.oeaw.ac.at.
3
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, 1030, Austria. claude.becker@gmi.oeaw.ac.at.

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.

KEYWORDS:

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

PMID:
28439857
DOI:
10.1007/978-1-4939-7003-2_5
[Indexed for MEDLINE]

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