Abstract. Manipulation of preimplantation embryos in vitro, such as in vitro fertilization (IVF), in vitro culture (IVC), intracytoplasmic sperm injection (ICSI), somatic cell nuclear transfer (SCNT) and other assisted reproduction technologies (ART), has contributed to the development of infertility treatment and new animal reproduction methods. However, such embryos often exhibit abnormal DNA methylation patterns in imprinted genes and centromeric satellite repeats. These DNA methylation patterns are established and maintained by three DNA methyltransferases: Dnmt1, Dnmt3a and Dnmt3b. Dnmt3b is responsible for the creation of methylation patterns during the early stage of embryogenesis and consists of many alternative splice variants that affect methylation activity; nevertheless, the roles of these variants have not yet been identified. In this study, we found an alternatively spliced variant of Dnmt3b lacking exon 6 (Dnmt3bΔ6) that is specific to mouse IVC embryos. Dnmt3bΔ6 also showed prominent expression in embryonic stem (ES) cells derived from in vitro manipulated embryos. Interestingly, IVC blastocysts were hypomethylated in centromeric satellite repeat regions that could be susceptible to methylation by Dnmt3b. In vitro methylation activity assays showed that Dnmt3bΔ6 had lower activity than normal Dnmt3b. Our findings suggest that Dnmt3bΔ6 could induce a hypomethylation status especially in in vitro manipulated embryos. Key words: DNA methylation, Dnmt3b, In vitro culture (J. Reprod. Dev. 57: 579-585, 2011) he 5th position cytosine residues in CpG sequences are often methylated in vertebrate genomic DNA [1]. DNA methylation plays an essential role in the normal development of mammalian embryos by regulating gene expression through genomic imprinting, X chromosome inactivation and genomic stability [2][3][4][5][6]. In vertebrates, two types of DNA methyltransferase activity have been reported, the de novo and maintenance types. In mice, de novo-type DNA methylation activity creates gene-specific methylation patterns during the implantation stage of embryogenesis, while maintenance-type activity ensures clonal transmission of lineage-specific methylation patterns during replication. Dnmt1 is responsible for the latter activity. On the other hand, two DNA methyltransferases, Dnmt3a and Dnmt3b, are responsible for creation of methylation patterns during the early stages of embryogenesis [7,8] and have been shown to possess de novo-type DNA methylation activity in vitro [9][10][11][12]. Recent studies have shown that Dnmts function in cooperation with each other to facilitate DNA methylation in both humans and mice [13][14][15].In mice, Dnmt3b is the major de novo DNA methyltransferase in E (embryonic stage) 4.5-7.5 embryos, and its expression is downregulated after midgestation [8,16]. Disruption of Dnmt3b results in embryonic lethality at E13.5 and hypomethylation of centromeric minor satellite repeats [8]. In humans, DNMT3B mutations have been shown to cause ICF (immunodeficiency, chromosomal instabi...