DNA methylation is an epigenetic mark essential for mammalian development, 
genomic stability, and imprinting. DNA methylation patterns are established and 
maintained by three DNA methyltransferases: DNMT1, DNMT3A, and DNMT3B. 
Interestingly, all three DNMTs make use of alternative splicing. DNMT3B has 
nearly 40 known splice variants expressed in a tissue- and disease-specific 
manner, but very little is known about the role of these splice variants in 
modulating DNMT3B function. We describe here the identification and 
characterization of a novel alternatively spliced form of DNMT3B lacking exon 5 
within the NH(2)-terminal regulatory domain. This variant, which we term 
DNMT3B3Delta5 because it is closely related in structure to the ubiquitously 
expressed DNMT3B3 isoform, is highly expressed in pluripotent cells and brain 
tissue, is downregulated during differentiation, and is conserved in the mouse. 
Creation of pluripotent iPS cells from fibroblasts results in marked induction 
of DNMT3B3Delta5. DNMT3B3Delta5 expression is also altered in human disease, 
with tumor cell lines displaying elevated or reduced expression depending on 
their tissue of origin. We then compared the DNA binding and subcellular 
localization of DNMT3B3Delta5 versus DNMT3B3, revealing that DNMT3B3Delta5 
possessed significantly enhanced DNA binding affinity and displayed an altered 
nuclear distribution. Finally, ectopic overexpression of DNMT3B3Delta5 resulted 
in repetitive element hypomethylation and enhanced cell growth in a colony 
formation assay. Taken together, these results show that DNMT3B3Delta5 may play 
an important role in stem cell maintenance or differentiation and suggest that 
sequences encoded by exon 5 influence the functional properties of DNMT3B.