Epigenetic natural variation in Arabidopsis thaliana

Matthew W. Vaughn, Milos Tanurdzić, Zachary Lippman, Hongmei Jiang, Robert Carrasquillo, Pablo D. Rabinowicz, Neilay Dedhia, W. Richard McCombie, Nicolas Agier, Agnès Bulski, Vincent Colot, R. W. Doerge, Robert A. Martienssen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

331 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1617-1629
Number of pages13
JournalPLoS biology
Volume5
Issue number7
DOIs
StatePublished - Jul 2007

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)

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