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

Rafael Yaari, Aviva Katz, Katherine Domb, Keith D. Harris, Assaf Zemach*, Nir Ohad

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


To properly regulate the genome, cytosine methylation is established by animal DNA methyltransferase 3 s (DNMT3s). While altered DNMT3 homologs, Domains rearranged methyltransferases (DRMs), have been shown to establish methylation via the RNA directed DNA methylation (RdDM) pathway, the role of true-plant DNMT3 orthologs remains elusive. Here, we profile de novo (RPS transgene) and genomic methylation in the basal plant, Physcomitrella patens, mutated in each of its PpDNMTs. We show 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; suggest that DRMs have emerged to target euchromatin; and link DNMT3 loss in angiosperms to the initiation of heterochromatic CHH methylation by CMT2.

Original languageEnglish
Article number1613
JournalNature Communications
Issue number1
StatePublished - 1 Dec 2019


FundersFunder number
Israeli Centers for Research Excellence Program of the Planning and Budgeting Committee, Israel Science Foundation757/12
Horizon 2020 Framework Programme679551
European Research Council
Israel Science Foundation767/09
Tel Aviv University


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