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Updated: Feb 28, 2026

Determination of DNA Methylation of Imprinted Genes in Arabidopsis Endosperm
Published on: January 28, 2011
Computational Analysis of Genome-Wide ARGONAUTE-Dependent DNA Methylation in Plants
Kai Tang1,2, Cheng-Guo Duan3,4, Huiming Zhang3
1Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. tang58@purdue.edu.
Abstract:
Whole-genome bisulfite sequencing (WGBS) has become a powerful tool to dissect genome-wide methylation profiles at single-base resolution. In this chapter we describe in detail the bioinformatics pipeline used for the analysis of ARGONAUTE-dependent DNA methylation in Arabidopsis thaliana. We provide tools and command lines used for mapping bisulfite sequencing reads, for estimating methylation levels at individual cytosine sites, for identifying differentially methylated regions (DMRs), and for calculating methylation levels of DMRs.

