RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs

Cytosine methylation is a key process in regulating genome function, established and maintained by DNA methyltransferases (DNMTs). DNMT3 known to establish methylation in mammals. While in plants, altered DNMT3 homologs, DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs), was shown to establish methylation via the RNA directed DNA methylation (RdDM) pathway, the role of true plant DNMT3 orthologs remained elusive.

To elucidate the role of plant DNMTs, we profiled genomic methylation and de novo methylation in the basal moss plant, Physcomitrella patens, mutated in each of its PpDNMTs.

To evaluate P. patens DNMTs role in de novo methylation, we introduced the repetitive DNA sequence (RPS) from Petunia hybrida , uncommon to P. patens. DNA methylation analysis of RPS in the first transgenic generation (T1), using bisulfite sequencing, reveal that RPS is methylated in WT cells in all three methylation contexts, CG, CHG, and CHH, implying on its ability to be de novo methylated in P. patens.

Furthermore, the methylation status of Ppdnmt mutants indicate, that PpDNMT3b mediates CG and CHH de novo methylation, independently of PpDRMs. Complementary de novo CHG methylation is specifically mediated by the CHROMOMETHYLASE, PpCMT. Intragenomically, PpDNMT3b functions preferentially within heterochromatin and is affected by PpCMT. In comparison, PpDRMs target active-euchromatic transposons.

Overall, our data resolve how DNA methylation in plants can be established in heterochromatin independently of RdDM pathway; suggest that DRMs have emerged to target euchromatin; and link DNMT3 loss in angiosperms to the initiation of heterochromatic CHH methylation by CMT2.

Ref: Yaari et al., Nat Commun. 2019, 6;10(1):2552.