DNMT3B gene is located on the long arm of chromosome 20 at position 11.2 and is composed of 23 exons and 22 introns. This gene encodes for a protein of 853 aa. DNMT3B gene is abundantly expressed in embryonic stem cells, but its expression is decreased upon their differentiation and remains low in adult somatic tissues.

Primary transcript of DNMT3B gene can be spliced five different mRNA isoforms that are DNMT3B1, DNMT3B2, DNMT3B3, DNMT3B4 and DNMT3B5.

DNMT3B protein is structured with N-terminal regulatory and C-terminal catalytic domains that are linked by repeated GK dipeptides (Glycine-Lysine-repeats). The N-terminal domain possesses nuclear localization signal sequence (NLS) responsible for nucleus DNMT3B localization. The N-terminal domain plays a regulatory role, and contains a proliferating cell nuclear antigen-binding domain. This N-domain also contains a cysteine rich zinc finger DNA binding motif (ATRX), a polybromo homology domain (PHD) targeting DNMT3B to the replication foci and a PWWP tetrapeptide chromatin-binding domain (Margot et al., 2000). The two halves are packed against each other to form a single structural module that exhibits a prominent positive electrostatic potential. The PWWP domain of DNMT3B alone binds DNA in vitro, probably through its basic surface, and DNMT3B binds DNA stronger than a mutant without the domain. In addition, the PWWP domain seems to target the de novo methyltransferases to chromatin. The C-terminal domain contains six conservative motifs I, IV, VI, VIII, IX and X. Motif I and X are involved in the formation of the S-adenosylomethionine binding site. Motif IV binds the substrate cytosine at the active site. Motif VI contains the glutamyl residue serving as a proton donor. Motif IX maintains the structure of the target recognition domain (TRD). Motif VIIIs function is unclear (Xie et al., 1999).
The intracellular distribution of DNMT3B enzyme is rather dynamic throughout the cell cycle, indeed this enzyme is diffusely distributed throughout the nucleoplasm during most of G1, associates with subnuclear sites of DNA replication during S-phase (Leonhardt et al.,1992), and binds to chromatin, with preference to pericentric heterochromatin, during G2 and M-phases (Easwaran et al., 2005).

853 amino acids; 95751 Da.

Nucleus.

DNMT3B is expressed at very low levels in most tissues except the testis, thyroid and bone marrow (Xie et al., 1999). DNMT3B level is profoundly increased in various tumor cell lines, indicating that it plays an important role in tumorigenesis (Robertson et al., 1999; Hermann et al., 2004). DNA methylation is a covalent chemical modification, resulting in the addition of a methyl (CH3) group at the carbon 5 position of the cytosine ring. DNMT3B uses S-adenosyl-L-methionine (AdoMet) as the source of the methyl group being transferred to the DNA bases. The methyl group of S-adenosylomethionine is bound to a sulphonium atom, which thermodynamically destabilizes the molecule and makes the relatively inert methylthiol of the methionine moiety very reactive towards nucleophilic attack by nitrogen, oxygen and sulphur atoms or activated C atoms (carbanions).
DNMT3B may also interact with DNMT1 and activate HDAC1, which deacetylates histones and represses gene transcription. This indicates that DNMT3B may be involved in chromatin remodeling associated with the modulation of gene transcription. DNMT3B can also effectively methylate C to m⁵C post-replicatively in unmethylated DNA. During or after replication, DNA regions may bind sequence-specific proteins which block the attachment of the methyl group to CpG dinucleotide and the formation of methylation patterns unique for each tissue. The existence of DNMT3B isoforms suggests that other factors can be involved in the binding of DNMT3B to a particular DNA region. Consequences of alternative splicing on DNMT3Bs ability to interact with DNMT3L. DNMT3L stimulates the catalytic activity of DNMT3A and DNMT3B methyltransferases (Suetake et al., 2004). DNMT3L binds to the carboxyl-terminal part of DNMT3B and increases the level of activity of this enzyme (Suetake et al., 2004).

DNMT3B exhibit a high degree of primary structure homology with DNMT3A. Structurally, DNMT3B and DNMT3A have a similar organization, with conserved domains: the long N-terminal region contains a PWWP domain and a cysteine-rich PHD zinc finger domain and the C-terminal catalytic domain. The same NLS and ATRX sequences were also founded in the DNMT3B and DNMT3A enzymes.

ICF syndrome (standing for Immunodeficiency, Centromere instability and Facial anomalies syndrome) is a rare autosomal recessive immune disorder caused by mutations of the gene DNMT3B. Therefore, the DNMT3B mutations, like A766P and R840Q, observed in patients are the likely underlying cause of their ICF phenotypes (Xie et al., 2006).
This hereditary syndrome is characterized by centromeric instability of chromosomes 1, 9, and 16 is associated with abnormal hypomethylation of CpG sites in their pericentromeric satellite regions (Hansen et al., 1999). At the molecular level, in patient DNA, sequences such as the pericentromeric classic satellite repeats of pericentromeric regions are hypomethylated, which attributes to reduced enzymatic activity of the mutant proteins (Jeanpierre et al., 1993; Gowher and Jeltsch, 2002).
Several polymorphisms were detected at the promoter region of DNMT3B gene and may influence its activity in DNA methylation and increase the susceptibility to several cancers. DNMT3B promoter polymorphisms influence on promoter hypermethylation of genes in other interacting pathways, such as cell cycle, apoptosis, or other DNA repair pathways and may increase level of DNA damage which contributes to an increased risk for cancers. For example, C>T (rs406193), -283T>C (rs121909506), -579G>T (rs2424909), -579G>T (rs2235758) and G39179T DNMT3B polymorphisms influence DNMT3B expression, thus contributing to the genetic susceptibility to different cancers (Lee et al., 2005; Fan et al., 2008; Montgomery et al., 2004; de Vogel et al., 2009; Daraei et al., 2011).
The common DNMT3B -149C>T (rs2424913) polymorphism was found to significantly increase DNTM3B promoter activity. This up-regulates the expression of the gene and may in turn lead to aberrant methylation of CpG islands in some tumor suppressor genes (Montgomery et al., 2004). It was associated with an increased risk for lung cancer (Shen et al., 2002), prostate cancer (Singal et al., 2005), and colorectal polyps, including colorectal adenomas (Jung et al., 2008), or with prognosis of head and neck cancer (Wang et al., 2004).