Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss‐of‐function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon‐derived, methylated at all cytosines, which may or may not form epialleles. We provide evidence that DNA sequence features such as density of CpGs and genomic repetitiveness of the loci predispose their susceptibility to epiallelic switching. The importance and predictive power of these genetic features were confirmed by analyses of common epialleles in natural Arabidopsis accessions, epigenetic recombinant inbred lines (epiRILs) and also verified in rice.
Why certain loci are able to stably switch between alternative epigenetic states (forming heritable epialleles), while others remain resistant to such switches seems to be predetermined by their genetic features, such as DNA sequence composition and repetitiveness.
Low‐copy number loci enriched in CG dinucleotides form transgenerationally stable epialleles.
High‐copy number loci depleted of CG nucleotides rapidly revert to one epiallelic form.
- Received September 9, 2016.
- Revision received December 9, 2016.
- Accepted December 9, 2016.
- © 2017 The Authors
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