Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development (PubMed:9662389, PubMed:11399089, PubMed:10555141, PubMed:11919202, PubMed:16567415, PubMed:17713477). DNA methylation is coordinated with methylation of histones (PubMed:9662389, PubMed:11399089, PubMed:10555141, PubMed:11919202, PubMed:16567415, PubMed:17713477). It modifies DNA in a non-processive manner and also methylates non-CpG sites (PubMed:9662389, PubMed:11399089, PubMed:10555141, PubMed:11919202, PubMed:16567415, PubMed:17713477). May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1 (PubMed:18823905). Plays a role in paternal and maternal imprinting (PubMed:15215868). Required for methylation of most imprinted loci in germ cells (PubMed:15215868). Acts as a transcriptional corepressor for ZBTB18 (PubMed:11350943). Recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites (PubMed:20547484). Can actively repress transcription through the recruitment of HDAC activity (PubMed:11350943). Also has weak auto-methylation activity on Cys-706 in absence of DNA (PubMed:21481189). a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + H(+) + S-adenosyl-L-homocysteine L-cysteinyl-[protein] + S-adenosyl-L-methionine = H(+) + S-adenosyl-L-homocysteine + S-methyl-L-cysteinyl-[protein] Activated by binding to the regulatory factor DNMT3L (PubMed:15671018, PubMed:17713477, PubMed:21481189). Auto-methylation at Cys-706 in absence of DNA inactivates the DNA methyltransferase activity (PubMed:21481189). Heterotetramer composed of 1 DNMT3A homodimer and 2 DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L) (By similarity). Interacts with DNMT1 and DNMT3B (By similarity). Interacts with MPHOSPH8 (By similarity). Interacts with histone H3 that is not methylated at 'Lys-4' (H3K4) (By similarity). Binds the ZBTB18 transcriptional repressor (PubMed:11350943). Interacts with SETDB1 (By similarity). Associates with HDAC1 through its ADD domain (PubMed:11350943, PubMed:12616525). Interacts with UHRF1 (PubMed:19798101). Interacts with the PRC2/EED-EZH2 complex (PubMed:16357870). Interacts with UBC9, PIAS1 and PIAS2 (PubMed:14752048). Interacts with SPOCD1 (PubMed:32674113). Interacts with ZNF263; recruited to the SIX3 promoter along with other proteins involved in chromatin modification and transcriptional corepression where it contributes to transcriptional repression (By similarity). Accumulates in the major satellite repeats at pericentric heterochromatin. Isoform 1 is expressed ubiquitously at low levels. Expression of isoform 2 is restricted to tissues containing cells which are undergoing active de novo methylation, including spleen, testis and thymus. At 7.5 dpc, the protein is moderately expressed in embryonic ectoderm and weakly in mesodermal cells. At 8.5 dpc and 9.5 dpc, the expression become ubiquitous with an increase in the somites and in the ventral part of the embryo. The PWWP domain is essential for targeting to pericentric heterochromatin. It specifically recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3) (PubMed:20547484). Auto-methylated at Cys-706: auto-methylation takes place in absence of DNA substrate and inactivates the DNA methyltransferase activity (PubMed:21481189). Inactivation by auto-methylation may be used to inactivate unused DNA methyltransferases in the cell (PubMed:21481189). Sumoylated; sumoylation disrupts the ability to interact with histone deacetylases (HDAC1 and HDAC2) and repress transcription. Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family. Truncated N-terminus.