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.
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References
Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, Bouchez D, Dillmann C, Guerche P, Hospital F, Colot V (2009) Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 5:e1000530
Reinders J, Wulff BB, Mirouze M, Marí-Ordóñez A, Dapp M, Rozhon W, Bucher E, Theiler G, Paszkowski J (2009) Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev 23:939–950
Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F (2012) Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc Natl Acad Sci USA 109:16240–16245.
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215–219
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536
Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC (2010) Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics 26:1000–1006
Laird PW (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11:191–203
Rabiner LR (1989) A tutorial on Hidden Markov Models and selected applications in speech recognition. Proc IEEE 77:257–286
Baum LE, Petrie T, Soules G, Weiss N (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann Math Stat 41:164–171
McLachlan GJ, Peel D (2000) Finite mixture models. John Wiley and Sons, Inc.
Viterbi AJ (1967) Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans Inf Theory 13:260–269
Johannes F, Colot V, Jansen RC (2008) Epigenome dynamics: a quantitative genetics perspective. Nat Rev Genet 9:883–890
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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Cortijo, S., Wardenaar, R., Colomé-Tatché, M., Johannes, F., Colot, V. (2014). Genome-Wide Analysis of DNA Methylation in Arabidopsis Using MeDIP-Chip. In: Spillane, C., McKeown, P. (eds) Plant Epigenetics and Epigenomics. Methods in Molecular Biology, vol 1112. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-773-0_9
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DOI: https://doi.org/10.1007/978-1-62703-773-0_9
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