Plant Epigenetics and Epigenomics pp 125-149 | Cite as
Genome-Wide Analysis of DNA Methylation in Arabidopsis Using MeDIP-Chip
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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.
Key words
DNA methylation 5-Methylcytosine (5mC) MeDIP Tiling array Epigenetic variationNotes
Acknowledgements
This work was supported in part by grants from the Agence Nationale de la Recherche (Genoplante TAG project, to V.C.) and by the European Union Network of Excellence “The Epigenome” (to V.C.). S.C. was supported by a Ph.D. studentship from the Ministère de l’Enseignement Supérieur et de la Recherche. R.W., M.C.-T., and F.J. were supported by grants from The Netherlands Organisation for Scientific Research.
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