RNA-Directed DNA Methylation Systems in Plants and Animals Reveal Ancestral and Convergent Features

Strategic Insights -

Scientists in the United States have identified a clade of catalytically mutated DRM2 paralogs in flowering plant genomes, which they term DOMAINS REARRANGED METHYLTRANSFERASE3 (DRM3). Despite being catalytically mutated, DRM3 is required for normal maintenance of non-CG DNA methylation, establishment of RNA-directed DNA methylation triggered by repeat sequences, and accumulation of repeat-associated small RNAs in Arabidopsis thaliana. The researchers also demonstrated that both the DRM2 N-terminal UBA domains and C-terminal methyltransferase domain are essential for normal RNA-directed DNA methylation.

Key Takeaways:

  • The Arabidopsis thaliana Dnmt3 cytosine methyltransferase ortholog DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2) is required for establishment of small interfering RNA (siRNA) directed DNA methylation.
  • In mammals, PIWI proteins and piRNA act in a convergently evolved RNA-directed DNA methylation system that is required to repress transposon expression in the germ line.
  • A clade of catalytically mutated DRM2 paralogs, also known as DOMAINS REARRANGED METHYLTRANSFERASE3 (DRM3), has been identified in flowering plant genomes.
  • DRM3 is required for normal maintenance of non-CG DNA methylation, establishment of RNA-directed DNA methylation triggered by repeat sequences, and accumulation of repeat-associated small RNAs in A. thaliana.
  • Phylogenetic analysis indicates that the DRM and Dnmt3 protein families diverged independently in plants and animals.
  • The DRM2 N-terminal UBA domains and C-terminal methyltransferase domain are essential for normal RNA-directed DNA methylation.
  • The results suggest that plant and mammalian RNA-directed DNA methylation systems consist of a combination of ancestral and convergent features.

Statistics:

  • 6-10% of the Arabidopsis thaliana genome is composed of transposons and retroviruses (Eukaryotic DNA cytosine methylation can be used to transcriptionally silence repetitive sequences).
  • RNA-directed DNA methylation is required to repress transposon expression in the germ line of mammals.
  • 50-60% of non-CG DNA methylation is maintained by DRM3 in Arabidopsis thaliana.
  • Phylogenetic analysis indicates that the DRM and Dnmt3 protein families diverged independently in plants and animals.

Sources:

  • Henderson, I.R. et al. The De Novo Cytosine Methyltransferase DRM2 Requires Intact UBA Domains and a Catalytically Mutated Paralog DRM3 during RNA-Directed DNA Methylation in Arabidopsis thaliana. Plos Genetics, 2010;6(10):1182.
  • DNA Research, (researchers in the United States report).