E3 ubiquitin-protein ligase. Participates in CpG methylation-dependent transcriptional regulation and epigenetic transcriptional silencing. Mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. Promotes methylation-mediated gene silencing leading, for example, to early flowering. Can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrate. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. Broadly distributed in the nucleus and enriched in the heterochromatic chromocenters. Expressed in inflorescences and leaves. The RING fingers are required for ubiquitin ligase activity. The YDG domain mediates the interaction with histone H3. Decreased DNA methylation primarily at CpG sites in genic regions, as well as repeated sequences in heterochromatic regions. Released transcriptional silencing at heterochromatin regions. Ectopic CpHpH methylation in the 5S rRNA genes against a background of CpG hypomethylation.