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Identification of Differentially Methylated Regions in the Genome of Arabidopsis thaliana

  • Kamal Kishore
  • Mattia Pelizzola
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1675)

Abstract

DNA methylation profiling in the epigenome of Arabidopsis thaliana (Arabidopsis) has provided great insights in the role of this epigenetic mark for the regulation of transcription in plants, and is often based on high-throughput sequencing. The analysis of these data involves a series of steps including quality checks, filtering, alignment, identification of methyl-cytosines, and the identification of differentially methylated regions. This chapter outlines the computational methodology required to profile genome-wide differential methylation patterns based on publicly available Arabidopsis base-resolution bisulfite sequencing data. The methylPipe Bioconductor package is adopted for the identification of the differentially methylated regions, and all the steps from the raw data to the required input are described in detail.

Key words

DNA methylation Bisulfite sequencing Computational biology DMRs methylPipe Arabidopsis 

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
  2. 2.Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK

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