Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip

Sandra Cortijo, René Wardenaar, Maria Colomé-Tatché, Frank Johannes, Vincent Colot

Research output: Contribution to journalArticleAcademicpeer-review

10 Citations (Scopus)

Abstract

DNA methylation is an epigenetic mark that is essential for preserving genome integrity and normal development in plants and mammals. Although this modification may serve a variety of purposes, it is best known for its role in stable transcriptional silencing of transposable elements and epigenetic regulation of some genes. In addition, it is increasingly recognized that alterations in DNA methylation patterns can sometimes be inherited across multiple generations and thus are a source of heritable phenotypic variation that is independent of any DNA sequence changes. With the advent of genomics, it is now possible to analyze DNA methylation genome-wide with high precision, which is a prerequisite for understanding fully the various functions and phenotypic impact of this modification. Indeed, several so-called epigenomic mapping methods have been developed for the analysis of DNA methylation. Among these, immunoprecipitation of methylated DNA followed by hybridization to genome tiling arrays (MeDIP-chip) arguably offers a reasonable compromise between cost, ease of implementation, and sensitivity to date. Here we describe the application of this method, from DNA extraction to data analysis, to the study of DNA methylation genome-wide in Arabidopsis.

Original languageEnglish
Pages (from-to)125-149
Number of pages25
JournalMethods in Molecular Biology
Volume1112
DOIs
Publication statusPublished - 2014

Keywords

  • Arabidopsis
  • DNA Methylation
  • DNA, Plant
  • Genomics
  • Markov Chains
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis
  • Quality Control

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