Patterns of population epigenomic diversity

• Published in: Nature (London) Vol. 495; no. 7440; pp. 193 - 198
• Main Authors: Schmitz, Robert J., Schultz, Matthew D., Urich, Mark A., Nery, Joseph R., Pelizzola, Mattia, Libiger, Ondrej, Alix, Andrew, McCosh, Richard B., Chen, Huaming, Schork, Nicholas J., Ecker, Joseph R.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 14.03.2013; Nature Publishing Group
• Subjects: 631/208/177; Analysis; Arabidopsis - genetics; Arabidopsis thaliana; Deoxyribonucleic acid; DNA; DNA methylation; DNA Methylation - genetics; DNA sequencing; DNA Transposable Elements - genetics; Epigenesis, Genetic - genetics; Epigenetic inheritance; Epigenomics; Gene mapping; Genes; Genetic aspects; Genetic diversity; Genetic research; Genetic variance; Genetic Variation - genetics; Genetics; Genome, Plant - genetics; Humanities and Social Sciences; Linkage Disequilibrium - genetics; multidisciplinary; Mutation; Nucleotide sequencing; Physiological aspects; Pollen; Pollen - genetics; Polymorphism, Genetic - genetics; Quantitative Trait Loci; RNA, Messenger - analysis; RNA, Messenger - genetics; RNA, Plant - genetics; Science; Seeds - genetics; United States
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature11968

Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures. A population epigenomic analysis of wild Arabidopsis thaliana accessions is presented, obtained by sequencing their whole genomes, methylomes and transcriptomes; thousands of DNA methylation variants are identified, some of which are associated with methylation quantitative trait loci. Patterns of population epigenomic diversity Like natural genetic variation, natural epigenetic variation — heritable alterations in gene expression caused by mechanisms other than changes in DNA sequence —is a source of phenotypic diversity. How epigenetic variants form and how genetic variation is linked to epigenetic variation at the population level, however, has been little studied. These authors present the first whole-genome, base-resolution, population-level epigenomic analysis by sequencing the genomes, methylomes and transcriptomes of a population of more than 150 accessions of the plant Arabidopsis thaliana isolated from across the Northern Hemisphere. Thousands of DNA-methylation variants were identified, many of them linked to genetic variants. The analyses also reveal that genes targeted by RNA-directed DNA methylation may have co-opted a mechanism that silences transposons to maintain their silenced state in vegetative tissues and to ensure correct expression in pollen, seed and germ line development.