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© 2007 Vaughn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Vaughn MW, Tanurdzi? M, Lippman Z, Jiang H, Carrasquillo R, et al. (2007) Epigenetic Natural Variation in Arabidopsis thaliana. PLoS Biol 5(7): e174. doi:10.1371/journal.pbio.0050174

Abstract

Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F2 families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means.

Details

Title
Epigenetic Natural Variation in Arabidopsis thaliana
Author
Vaughn, Matthew W; Tanurdzic, Milos; Lippman, Zachary; Jiang, Hongmei; Carrasquillo, Robert; Rabinowicz, Pablo D; Dedhia, Neilay; McCombie, W Richard; Agier, Nicolas; Bulski, Agnès; Colot, Vincent; Doerge, RW; Martienssen, Robert A
Pages
e174
Section
Research Article
Publication year
2007
Publication date
Jul 2007
Publisher
Public Library of Science
ISSN
15449173
e-ISSN
15457885
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1292204453
Copyright
© 2007 Vaughn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Vaughn MW, Tanurdzi? M, Lippman Z, Jiang H, Carrasquillo R, et al. (2007) Epigenetic Natural Variation in Arabidopsis thaliana. PLoS Biol 5(7): e174. doi:10.1371/journal.pbio.0050174