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Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

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Becker,  C
Max Planck Institute for Developmental Biology, Max Planck Society;

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Hagmann,  J
Max Planck Institute for Developmental Biology, Max Planck Society;

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Müller,  J
Max Planck Institute for Developmental Biology, Max Planck Society;

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Koenig,  D
Max Planck Institute for Developmental Biology, Max Planck Society;

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Stegle,  O
Former Research Group Machine Learning and Computational Biology, Max Planck Institute for Intelligent Systems, Max Planck Society;

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Borgwardt,  K
Former Research Group Machine Learning and Computational Biology, Max Planck Institute for Intelligent Systems, Max Planck Society;

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Weigel,  D
Max Planck Institute for Developmental Biology, Max Planck Society;

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Citation

Becker, C., Hagmann, J., Müller, J., Koenig, D., Stegle, O., Borgwardt, K., et al. (2011). Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature, 480(7376), 245-249. doi:10.1038/nature10555.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0013-B8CE-B
Abstract
Heritable epigenetic polymorphisms, such as differential cytosine methylation, can underlie phenotypic variation1, 2. Moreover, wild strains of the plant Arabidopsis thaliana differ in many epialleles3, 4, and these can influence the expression of nearby genes1, 2. However, to understand their role in evolution5, it is imperative to ascertain the emergence rate and stability of epialleles, including those that are not due to structural variation. We have compared genome-wide DNA methylation among 10 A. thaliana lines, derived 30 generations ago from a common ancestor6. Epimutations at individual positions were easily detected, and close to 30,000 cytosines in each strain were differentially methylated. In contrast, larger regions of contiguous methylation were much more stable, and the frequency of changes was in the same low range as that of DNA mutations7. Like individual positions, the same regions were often affected by differential methylation in independent lines, with evidence for recurrent cycles of forward and reverse mutations. Transposable elements and short interfering RNAs have been causally linked to DNA methylation8. In agreement, differentially methylated sites were farther from transposable elements and showed less association with short interfering RNA expression than invariant positions. The biased distribution and frequent reversion of epimutations have important implications for the potential contribution of sequence-independent epialleles to plant evolution.