Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts

PLoS One. 2012;7(9):e45242. doi: 10.1371/journal.pone.0045242. Epub 2012 Sep 20.


Individual plants within a population may vary at both genetic and epigenetic levels. The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of mechanisms that faithfully maintain epigenetic marks, epigenetic differences are more frequent than genetic variation. Epigenetically divergent stretches of isogenic DNA sequence are called epialleles. Currently, it is not clear why certain regions exhibit variable epigenetic status. We identified and characterised two long RNA transcripts with altered expression and DNA methylation in an ago5 mutant. However, further investigation revealed that these changes were not dependent upon AGO5. Rather, the variable transcription of these loci in Arabidopsis mutant and wild-type populations corresponds to spontaneous differential methylated regions (DMRs) or epialleles. These two DMRs are delineated by RNAs which are highly expressed when the DMR is hypomethylated. Furthermore, they control the expression of 5' transcriptional start site mRNA variants of nearby protein coding genes. Our data support the recent observations that meiotically stable DMRs exist within inbred populations. We further demonstrate that DMR boundaries can be defined by putative non-coding promoter-associated transcripts.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics
  • DNA Methylation
  • DNA, Plant / genetics*
  • Epigenesis, Genetic*
  • Genetic Loci
  • Genetic Variation
  • Genetics, Population
  • Genotype
  • Mutation
  • Promoter Regions, Genetic*
  • RNA, Messenger / genetics*
  • RNA, Untranslated / genetics*
  • RNA-Binding Proteins / genetics


  • Arabidopsis Proteins
  • DNA, Plant
  • RNA, Messenger
  • RNA, Untranslated
  • RNA-Binding Proteins
  • argonaute 5 protein, Arabidopsis

Grant support

PF was supported by a short term EMBO fellowship ASTF158-2008. This work was supported by the Gatsby Charitable Foundation and the European Union Sixth Framework Programme Integrated Project SIROCCO (LSHG-CT-2006-037900). DCB was supported as a Royal Society Research Professor. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.