Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing. In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Functions as a transcriptional corepressor by associating with ZHX1 (By similarity). Required for DUX4 silencing in somatic cells (By similarity). a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + H(+) + S-adenosyl-L-homocysteine Activated by binding to the regulatory factor DNMT3L. Interacts with CBX4, DNMT1, DNMT3A, SETDB1, UBE2I9, UBL1 and ZHX1 (By similarity). Interacts with SUV39H1 and BAZ2A/TIP5. Interacts with the PRC2/EED-EZH2 complex. Interacts with UHRF1. Accumulates in the major satellite repeats at pericentric heterochromatin. Expressed in almost all blastocysts at 3.0 dpc. Preferentially expressed in the trophectoderm (TE) in 3.5 dpc and polar TE in 4.0 dpc blastocysts. In 4.5 dpc embryos, expressed in the polar TE and some inner cell mass (ICM) embryonic lineage cells. In post-implantation embryo at 5.5 dpc, expressed in the epiblast (embryonic lineage) derived from the ICM. Highly expressed, at 7.5 dpc, in the embryonic ectoderm, neural ectoderm, and chorionic ectoderm; a weak expression is also detected in mesodermal and endodermal cells. At later stages, the expression is detected predominantly in the forebrain and eyes but weakly throughout the embryo. The PWWP domain is essential for targeting to pericentric heterochromatin. Sumoylated. Citrullinated by PADI4. Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.